diff --git a/.gitattributes b/.gitattributes
index e69de29bb..c3cdc1f56 100644
--- a/.gitattributes
+++ b/.gitattributes
@@ -0,0 +1,2 @@
+pixi.lock merge=binary linguist-language=YAML linguist-generated=true
+Cargo.lock merge=binary linguist-generated=true
diff --git a/.github/workflows/python-bindings.yml b/.github/workflows/python-bindings.yml
index b3bb161df..a5c620d47 100644
--- a/.github/workflows/python-bindings.yml
+++ b/.github/workflows/python-bindings.yml
@@ -35,6 +35,7 @@ jobs:
       - uses: prefix-dev/setup-pixi@v0.8.3
         with:
           manifest-path: py-rattler/pixi.toml
+          environments: test
       - uses: actions-rust-lang/setup-rust-toolchain@v1
         with:
           components: clippy, rustfmt
@@ -44,6 +45,9 @@ jobs:
           pixi run -e test lint
           pixi run -e test fmt-check
       - name: Run tests
+        env:
+          RATTLER_TEST_R2_ACCESS_KEY_ID: ${{ secrets.RATTLER_TEST_R2_ACCESS_KEY_ID }}
+          RATTLER_TEST_R2_SECRET_ACCESS_KEY: ${{ secrets.RATTLER_TEST_R2_SECRET_ACCESS_KEY }}
         run: |
           cd py-rattler
           pixi run -e test test --color=yes
diff --git a/Cargo.toml b/Cargo.toml
index ba1fde538..8edd7baf0 100644
--- a/Cargo.toml
+++ b/Cargo.toml
@@ -52,6 +52,7 @@ chrono = { version = "0.4.39", default-features = false, features = [
     "alloc",
 ] }
 clap = { version = "4.5.29", features = ["derive"] }
+clap-verbosity-flag = "3.0.1"
 cmake = "0.1.54"
 console = { version = "0.15.10", features = ["windows-console-colors"] }
 criterion = "0.5"
@@ -105,6 +106,7 @@ memmap2 = "0.9.5"
 netrc-rs = "0.1.2"
 nom = "7.1.3"
 num_cpus = "1.16.0"
+opendal = { version = "0.51.2", default-features = false }
 once_cell = "1.20.3"
 ouroboros = "0.18.5"
 parking_lot = "0.12.3"
@@ -161,6 +163,7 @@ tokio-util = "0.7.13"
 tower = { version = "0.5.2", default-features = false }
 tower-http = { version = "0.6.2", default-features = false }
 tracing = "0.1.41"
+tracing-log = "0.2.0"
 tracing-subscriber = { version = "0.3.19", default-features = false }
 tracing-test = { version = "0.2.5" }
 trybuild = { version = "1.0.103" }
diff --git a/crates/rattler_conda_types/Cargo.toml b/crates/rattler_conda_types/Cargo.toml
index 580641364..2afab5ba9 100644
--- a/crates/rattler_conda_types/Cargo.toml
+++ b/crates/rattler_conda_types/Cargo.toml
@@ -24,17 +24,25 @@ itertools = { workspace = true }
 lazy-regex = { workspace = true }
 nom = { workspace = true }
 purl = { workspace = true, features = ["serde"] }
-rattler_digest = { path = "../rattler_digest", version = "1.0.6", default-features = false, features = ["serde"] }
+rattler_digest = { path = "../rattler_digest", version = "1.0.6", default-features = false, features = [
+  "serde",
+] }
 rattler_macros = { path = "../rattler_macros", version = "1.0.6", default-features = false }
+rattler_redaction = { version = "0.1.6", path = "../rattler_redaction", default-features = false }
 regex = { workspace = true }
-simd-json = { workspace = true , features = ["serde_impl"]}
+simd-json = { workspace = true, features = ["serde_impl"] }
 serde = { workspace = true, features = ["derive", "rc"] }
 serde_json = { workspace = true }
 serde_repr = { workspace = true }
 serde_with = { workspace = true, features = ["indexmap_2"] }
 serde-untagged = { workspace = true }
 serde_yaml = { workspace = true }
-smallvec = { workspace = true, features = ["serde", "const_new", "const_generics", "union"] }
+smallvec = { workspace = true, features = [
+  "serde",
+  "const_new",
+  "const_generics",
+  "union",
+] }
 strum = { workspace = true, features = ["derive"] }
 tempfile = { workspace = true }
 thiserror = { workspace = true }
@@ -42,15 +50,22 @@ tracing = { workspace = true }
 typed-path = { workspace = true }
 url = { workspace = true, features = ["serde"] }
 indexmap = { workspace = true }
-rattler_redaction = { version = "0.1.6", path = "../rattler_redaction" }
 dirs = { workspace = true }
 rayon = { workspace = true, optional = true }
 fs-err = { workspace = true }
 
 [dev-dependencies]
 rand = { workspace = true }
-insta = { workspace = true, features = ["yaml", "redactions", "toml", "glob", "filters"] }
-rattler_package_streaming = { path = "../rattler_package_streaming", default-features = false, features = ["rustls-tls"] }
+insta = { workspace = true, features = [
+  "yaml",
+  "redactions",
+  "toml",
+  "glob",
+  "filters",
+] }
+rattler_package_streaming = { path = "../rattler_package_streaming", default-features = false, features = [
+  "rustls-tls",
+] }
 rstest = { workspace = true }
 assert_matches = { workspace = true }
 hex-literal = { workspace = true }
diff --git a/crates/rattler_index/Cargo.toml b/crates/rattler_index/Cargo.toml
index d3157f28c..7c235b212 100644
--- a/crates/rattler_index/Cargo.toml
+++ b/crates/rattler_index/Cargo.toml
@@ -3,23 +3,64 @@ name = "rattler_index"
 version = "0.20.13"
 edition.workspace = true
 authors = []
-description = "A crate that indexes directories containing conda packages to create local conda channels"
+description = "A crate to index conda channels and create a repodata.json file."
 categories.workspace = true
 homepage.workspace = true
 repository.workspace = true
 license.workspace = true
 readme.workspace = true
+default-run = "rattler-index"
+
+[features]
+default = ["rustls-tls"]
+native-tls = [
+  "reqwest/native-tls",
+  "reqwest/native-tls-alpn",
+  "rattler_package_streaming/native-tls",
+  "rattler_networking/native-tls",
+  "tools/native-tls",
+]
+rustls-tls = [
+  "reqwest/rustls-tls",
+  "reqwest/rustls-tls-native-roots",
+  "rattler_package_streaming/rustls-tls",
+  "rattler_networking/rustls-tls",
+  "tools/rustls-tls",
+]
+
+[[bin]]
+name = "rattler-index"
+path = "src/main.rs"
 
 [dependencies]
+anyhow = { workspace = true }
+clap = { workspace = true, features = ["derive", "env"] }
+clap-verbosity-flag = { workspace = true }
+console = { workspace = true }
 fs-err = { workspace = true }
-rattler_conda_types = { path="../rattler_conda_types", version = "0.31.0", default-features = false }
-rattler_digest = { path="../rattler_digest", version = "1.0.6", default-features = false }
-rattler_package_streaming = { path="../rattler_package_streaming", version = "0.22.29", default-features = false }
+fxhash = { workspace = true }
+futures = { workspace = true }
+indicatif = { workspace = true }
+opendal = { workspace = true, features = [
+  "services-s3",
+  "services-fs",
+], default-features = false }
+rattler_networking = { path = "../rattler_networking", version = "0.22.4", default-features = false }
+rattler_conda_types = { path = "../rattler_conda_types", version = "0.31.0" }
+rattler_digest = { path = "../rattler_digest", version = "1.0.6", default-features = false }
+rattler_package_streaming = { path = "../rattler_package_streaming", version = "0.22.29", default-features = false }
+reqwest = { workspace = true, default-features = false, features = [
+  "http2",
+  "macos-system-configuration",
+  "charset",
+] }
 serde_json = { workspace = true }
-tempfile = { workspace = true }
+tokio = { workspace = true, features = ["full"] }
 tracing = { workspace = true }
-walkdir = { workspace = true }
+tracing-subscriber = { workspace = true, features = ["env-filter", "fmt"] }
+tracing-log = { workspace = true }
+url = { workspace = true }
 
 [dev-dependencies]
 tempfile = { workspace = true }
-tools = { path = "../tools" }
+tools = { path = "../tools", default-features = false }
diff --git a/crates/rattler_index/src/lib.rs b/crates/rattler_index/src/lib.rs
index 37bdac722..6ea2c85dc 100644
--- a/crates/rattler_index/src/lib.rs
+++ b/crates/rattler_index/src/lib.rs
@@ -2,31 +2,43 @@
 //! files
 #![deny(missing_docs)]
 
-use fs_err as fs;
+use anyhow::Result;
+use fs_err::{self as fs};
+use futures::future::try_join_all;
+use fxhash::FxHashMap;
+use indicatif::{MultiProgress, ProgressBar, ProgressStyle};
 use rattler_conda_types::{
     package::{ArchiveType, IndexJson, PackageFile},
     ChannelInfo, PackageRecord, Platform, RepoData,
 };
+use rattler_networking::{Authentication, AuthenticationStorage};
 use rattler_package_streaming::{read, seek};
 use std::{
     collections::{HashMap, HashSet},
-    ffi::OsStr,
-    io::{Read, Write},
+    io::{Cursor, Read},
     path::{Path, PathBuf},
+    str::FromStr,
+    sync::Arc,
+};
+use tokio::sync::Semaphore;
+use url::Url;
+
+use opendal::{
+    services::{FsConfig, S3Config},
+    Configurator, Operator,
 };
-use tempfile::NamedTempFile;
-use walkdir::WalkDir;
 
 /// Extract the package record from an `index.json` file.
 pub fn package_record_from_index_json<T: Read>(
-    file: &Path,
+    package_as_bytes: impl AsRef<[u8]>,
     index_json_reader: &mut T,
 ) -> std::io::Result<PackageRecord> {
     let index = IndexJson::from_reader(index_json_reader)?;
 
-    let sha256_result = rattler_digest::compute_file_digest::<rattler_digest::Sha256>(file)?;
-    let md5_result = rattler_digest::compute_file_digest::<rattler_digest::Md5>(file)?;
-    let size = fs::metadata(file)?.len();
+    let sha256_result =
+        rattler_digest::compute_bytes_digest::<rattler_digest::Sha256>(&package_as_bytes);
+    let md5_result = rattler_digest::compute_bytes_digest::<rattler_digest::Md5>(&package_as_bytes);
+    let size = package_as_bytes.as_ref().len();
 
     let package_record = PackageRecord {
         name: index.name,
@@ -36,7 +48,7 @@ pub fn package_record_from_index_json<T: Read>(
         subdir: index.subdir.unwrap_or_else(|| "unknown".to_string()),
         md5: Some(md5_result),
         sha256: Some(sha256_result),
-        size: Some(size),
+        size: Some(size as u64),
         arch: index.arch,
         platform: index.platform,
         depends: index.depends,
@@ -63,12 +75,21 @@ pub fn package_record_from_index_json<T: Read>(
 /// and extract the package record from it.
 pub fn package_record_from_tar_bz2(file: &Path) -> std::io::Result<PackageRecord> {
     let reader = fs::File::open(file)?;
+    package_record_from_tar_bz2_reader(reader)
+}
+
+/// Extract the package record from a `.tar.bz2` package file.
+/// This function will look for the `info/index.json` file in the conda package
+/// and extract the package record from it.
+pub fn package_record_from_tar_bz2_reader(reader: impl Read) -> std::io::Result<PackageRecord> {
+    let bytes = reader.bytes().collect::<Result<Vec<u8>, _>>()?;
+    let reader = Cursor::new(bytes.clone());
     let mut archive = read::stream_tar_bz2(reader);
     for entry in archive.entries()?.flatten() {
         let mut entry = entry;
         let path = entry.path()?;
         if path.as_os_str().eq("info/index.json") {
-            return package_record_from_index_json(file, &mut entry);
+            return package_record_from_index_json(bytes, &mut entry);
         }
     }
     Err(std::io::Error::new(
@@ -82,13 +103,22 @@ pub fn package_record_from_tar_bz2(file: &Path) -> std::io::Result<PackageRecord
 /// and extract the package record from it.
 pub fn package_record_from_conda(file: &Path) -> std::io::Result<PackageRecord> {
     let reader = fs::File::open(file)?;
+    package_record_from_conda_reader(reader)
+}
+
+/// Extract the package record from a `.conda` package file content.
+/// This function will look for the `info/index.json` file in the conda package
+/// and extract the package record from it.
+pub fn package_record_from_conda_reader(reader: impl Read) -> std::io::Result<PackageRecord> {
+    let bytes = reader.bytes().collect::<Result<Vec<u8>, _>>()?;
+    let reader = Cursor::new(bytes.clone());
     let mut archive = seek::stream_conda_info(reader).expect("Could not open conda file");
 
     for entry in archive.entries()?.flatten() {
         let mut entry = entry;
         let path = entry.path()?;
         if path.as_os_str().eq("info/index.json") {
-            return package_record_from_index_json(file, &mut entry);
+            return package_record_from_index_json(bytes, &mut entry);
         }
     }
     Err(std::io::Error::new(
@@ -97,117 +127,319 @@ pub fn package_record_from_conda(file: &Path) -> std::io::Result<PackageRecord>
     ))
 }
 
-/// Create a new `repodata.json` for all packages in the given output folder. If
-/// `target_platform` is `Some`, only that specific subdir is indexed. Otherwise
-/// indexes all subdirs and creates a `repodata.json` for each.
-pub fn index(output_folder: &Path, target_platform: Option<&Platform>) -> std::io::Result<()> {
-    let entries = WalkDir::new(output_folder).into_iter();
-    let entries: Vec<(PathBuf, ArchiveType)> = entries
-        .filter_entry(|e| e.depth() <= 2)
-        .filter_map(Result::ok)
-        .filter_map(|e| {
-            ArchiveType::split_str(e.path().to_string_lossy().as_ref())
-                .map(|(p, t)| (PathBuf::from(format!("{}{}", p, t.extension())), t))
+async fn index_subdir(
+    subdir: Platform,
+    op: Operator,
+    force: bool,
+    progress: MultiProgress,
+    semaphore: Arc<Semaphore>,
+) -> Result<()> {
+    let mut registered_packages: FxHashMap<String, PackageRecord> = HashMap::default();
+    if !force {
+        let repodata_path = format!("{subdir}/repodata.json");
+        let repodata_bytes = op.read(&repodata_path).await;
+        let repodata: RepoData = match repodata_bytes {
+            Ok(bytes) => serde_json::from_slice(&bytes.to_vec())?,
+            Err(e) => {
+                if e.kind() != opendal::ErrorKind::NotFound {
+                    return Err(e.into());
+                }
+                tracing::info!("Could not find repodata.json. Creating new one.");
+                RepoData {
+                    info: Some(ChannelInfo {
+                        subdir: subdir.to_string(),
+                        base_url: None,
+                    }),
+                    packages: HashMap::default(),
+                    conda_packages: HashMap::default(),
+                    removed: HashSet::default(),
+                    version: Some(2),
+                }
+            }
+        };
+        registered_packages.extend(repodata.packages.into_iter());
+        registered_packages.extend(repodata.conda_packages.into_iter());
+        tracing::debug!(
+            "Found {} already registered packages in {}/repodata.json.",
+            registered_packages.len(),
+            subdir
+        );
+    }
+    let uploaded_packages: HashSet<String> = op
+        .list_with(&format!("{}/", subdir.as_str()))
+        .await?
+        .iter()
+        .filter_map(|entry| {
+            if entry.metadata().mode().is_file() {
+                let filename = entry.name().to_string();
+                // Check if the file is an archive package file.
+                ArchiveType::try_from(&filename).map(|_| filename)
+            } else {
+                None
+            }
         })
         .collect();
 
-    // find all subdirs
-    let mut platforms = entries
+    tracing::debug!(
+        "Found {} already uploaded packages in subdir {}.",
+        uploaded_packages.len(),
+        subdir
+    );
+
+    let packages_to_delete = registered_packages
+        .keys()
+        .cloned()
+        .collect::<HashSet<_>>()
+        .difference(&uploaded_packages)
+        .cloned()
+        .collect::<Vec<_>>();
+
+    tracing::debug!(
+        "Deleting {} packages from subdir {}.",
+        packages_to_delete.len(),
+        subdir
+    );
+
+    for filename in packages_to_delete {
+        registered_packages.remove(&filename);
+    }
+
+    let packages_to_add = uploaded_packages
+        .difference(&registered_packages.keys().cloned().collect::<HashSet<_>>())
+        .cloned()
+        .collect::<Vec<_>>();
+
+    tracing::debug!(
+        "Adding {} packages to subdir {}.",
+        packages_to_add.len(),
+        subdir
+    );
+
+    let pb = Arc::new(progress.add(ProgressBar::new(packages_to_add.len() as u64)));
+    let sty = ProgressStyle::with_template(
+        "[{elapsed_precise}] {bar:40.cyan/blue} {pos:>7}/{len:7} {msg}",
+    )
+    .unwrap()
+    .progress_chars("##-");
+    pb.set_style(sty);
+
+    let tasks = packages_to_add
         .iter()
-        .filter_map(|(p, _)| {
-            p.parent().and_then(Path::file_name).and_then(|file_name| {
-                let name = file_name.to_string_lossy().to_string();
-                if name == "src_cache" {
-                    None
-                } else {
-                    Some(name)
+        .map(|filename| {
+            tokio::spawn({
+                let op = op.clone();
+                let filename = filename.clone();
+                let pb = pb.clone();
+                let semaphore = semaphore.clone();
+                {
+                    async move {
+                        let _permit = semaphore
+                            .acquire()
+                            .await
+                            .expect("Semaphore was unexpectedly closed");
+                        pb.set_message(format!(
+                            "Indexing {} {}",
+                            subdir.as_str(),
+                            console::style(filename.clone()).dim()
+                        ));
+                        let file_path = format!("{subdir}/{filename}");
+                        let buffer = op.read(&file_path).await?;
+                        let bytes = buffer.to_vec();
+                        let cursor = Cursor::new(bytes);
+                        // We already know it's not None
+                        let archive_type = ArchiveType::try_from(&filename).unwrap();
+                        let record = match archive_type {
+                            ArchiveType::TarBz2 => package_record_from_tar_bz2_reader(cursor),
+                            ArchiveType::Conda => package_record_from_conda_reader(cursor),
+                        }?;
+                        pb.inc(1);
+                        Ok::<(String, PackageRecord), std::io::Error>((filename.clone(), record))
+                    }
                 }
             })
         })
-        .collect::<std::collections::HashSet<_>>();
+        .collect::<Vec<_>>();
+    let results = try_join_all(tasks).await?;
 
-    // Always create noarch subdir
-    if !output_folder.join("noarch").exists() {
-        fs::create_dir(output_folder.join("noarch"))?;
-    }
+    pb.finish_with_message(format!("Finished {}", subdir.as_str()));
 
-    // Make sure that we index noarch if it is not already indexed
-    if !output_folder.join("noarch/repodata.json").exists() {
-        platforms.insert("noarch".to_string());
-    }
+    tracing::debug!(
+        "Successfully added {} packages to subdir {}.",
+        results.len(),
+        subdir
+    );
 
-    // Create target platform dir if needed
-    if let Some(target_platform) = target_platform {
-        let platform_str = target_platform.to_string();
-        if !output_folder.join(&platform_str).exists() {
-            fs::create_dir(output_folder.join(&platform_str))?;
-            platforms.insert(platform_str);
-        }
+    for result in results {
+        let (filename, record) = result?;
+        registered_packages.insert(filename, record);
     }
 
-    for platform in platforms {
-        if let Some(target_platform) = target_platform {
-            if platform != target_platform.to_string() {
-                if platform == "noarch" {
-                    // check that noarch is already indexed if it is not the target platform
-                    if output_folder.join("noarch/repodata.json").exists() {
-                        continue;
-                    }
-                } else {
-                    continue;
-                }
+    let mut packages: FxHashMap<String, PackageRecord> = HashMap::default();
+    let mut conda_packages: FxHashMap<String, PackageRecord> = HashMap::default();
+    for (filename, package) in registered_packages {
+        match ArchiveType::try_from(&filename) {
+            Some(ArchiveType::TarBz2) => {
+                packages.insert(filename, package);
             }
+            Some(ArchiveType::Conda) => {
+                conda_packages.insert(filename, package);
+            }
+            _ => panic!("Unknown archive type"),
         }
+    }
 
-        let mut repodata = RepoData {
-            info: Some(ChannelInfo {
-                subdir: platform.clone(),
-                base_url: None,
-            }),
-            packages: HashMap::default(),
-            conda_packages: HashMap::default(),
-            removed: HashSet::default(),
-            version: Some(2),
-        };
+    let repodata = RepoData {
+        info: Some(ChannelInfo {
+            subdir: subdir.to_string(),
+            base_url: None,
+        }),
+        packages,
+        conda_packages,
+        removed: HashSet::default(),
+        version: Some(2),
+    };
 
-        for (p, t) in entries.iter().filter_map(|(p, t)| {
-            p.parent().and_then(|parent| {
-                parent.file_name().and_then(|file_name| {
-                    if file_name == OsStr::new(&platform) {
-                        // If the file_name is the platform we're looking for, return Some((p, t))
-                        Some((p, t))
-                    } else {
-                        // Otherwise, we return None to filter out this item
-                        None
-                    }
-                })
-            })
-        }) {
-            let record = match t {
-                ArchiveType::TarBz2 => package_record_from_tar_bz2(p),
-                ArchiveType::Conda => package_record_from_conda(p),
-            };
-            let (Ok(record), Some(file_name)) = (record, p.file_name()) else {
-                tracing::info!("Could not read package record from {:?}", p);
-                continue;
-            };
-            match t {
-                ArchiveType::TarBz2 => repodata
-                    .packages
-                    .insert(file_name.to_string_lossy().to_string(), record),
-                ArchiveType::Conda => repodata
-                    .conda_packages
-                    .insert(file_name.to_string_lossy().to_string(), record),
-            };
+    let repodata_path = format!("{subdir}/repodata.json");
+    let repodata_bytes = serde_json::to_vec(&repodata)?;
+    op.write(&repodata_path, repodata_bytes).await?;
+    // todo: also write repodata.json.bz2, repodata.json.zst, repodata.json.jlap and sharded repodata once available in rattler
+    // https://github.com/conda/rattler/issues/1096
+
+    Ok(())
+}
+
+/// Create a new `repodata.json` for all packages in the channel at the given directory.
+pub async fn index_fs(
+    channel: impl Into<PathBuf>,
+    target_platform: Option<Platform>,
+    force: bool,
+    max_parallel: usize,
+) -> anyhow::Result<()> {
+    let mut config = FsConfig::default();
+    config.root = Some(channel.into().canonicalize()?.to_string_lossy().to_string());
+    index(target_platform, config, force, max_parallel).await
+}
+
+/// Create a new `repodata.json` for all packages in the channel at the given S3 URL.
+#[allow(clippy::too_many_arguments)]
+pub async fn index_s3(
+    channel: Url,
+    region: String,
+    endpoint_url: Url,
+    force_path_style: bool,
+    access_key_id: Option<String>,
+    secret_access_key: Option<String>,
+    session_token: Option<String>,
+    target_platform: Option<Platform>,
+    force: bool,
+    max_parallel: usize,
+) -> anyhow::Result<()> {
+    let mut s3_config = S3Config::default();
+    s3_config.root = Some(channel.path().to_string());
+    s3_config.bucket = channel
+        .host_str()
+        .ok_or(anyhow::anyhow!("No bucket in S3 URL"))?
+        .to_string();
+    s3_config.region = Some(region);
+    s3_config.endpoint = Some(endpoint_url.to_string());
+    s3_config.enable_virtual_host_style = !force_path_style;
+    // Use credentials from the CLI if they are provided.
+    if let (Some(access_key_id), Some(secret_access_key)) = (access_key_id, secret_access_key) {
+        s3_config.secret_access_key = Some(secret_access_key);
+        s3_config.access_key_id = Some(access_key_id);
+        s3_config.session_token = session_token;
+    } else {
+        // If they're not provided, check rattler authentication storage for credentials.
+        let auth_storage = AuthenticationStorage::from_env_and_defaults()?;
+        let auth = auth_storage.get_by_url(channel)?;
+        if let (
+            _,
+            Some(Authentication::S3Credentials {
+                access_key_id,
+                secret_access_key,
+                session_token,
+            }),
+        ) = auth
+        {
+            s3_config.access_key_id = Some(access_key_id);
+            s3_config.secret_access_key = Some(secret_access_key);
+            s3_config.session_token = session_token;
         }
+    }
+    index(target_platform, s3_config, force, max_parallel).await
+}
+
+/// Create a new `repodata.json` for all packages in the given configurator's root.
+/// If `target_platform` is `Some`, only that specific subdir is indexed.
+/// Otherwise indexes all subdirs and creates a `repodata.json` for each.
+///
+/// The process is the following:
+/// 1. Get all subdirs and create `noarch` and `target_platform` if they do not exist.
+/// 2. Iterate subdirs and index each subdir.
+///    Therefore, we need to:
+///    1. Collect all uploaded packages in subdir
+///    2. Collect all registered packages from `repodata.json` (if exists)
+///    3. Determine which packages to add to and to delete from `repodata.json`
+///    4. Write `repodata.json` back
+pub async fn index<T: Configurator>(
+    target_platform: Option<Platform>,
+    config: T,
+    force: bool,
+    max_parallel: usize,
+) -> anyhow::Result<()> {
+    let builder = config.into_builder();
+
+    // Get all subdirs
+    let op = Operator::new(builder)?.finish();
+    let entries = op.list_with("").await?;
+    let mut subdirs = entries
+        .iter()
+        .filter_map(|entry| {
+            if entry.metadata().mode().is_dir() && entry.name() != "/" {
+                // Directory entries always end with `/`.
+                Some(entry.name().trim_end_matches('/').to_string())
+            } else {
+                None
+            }
+        })
+        .map(|s| Platform::from_str(&s))
+        .collect::<Result<HashSet<_>, _>>()?;
 
-        let mut out_file =
-            NamedTempFile::with_prefix_in("repodata-", output_folder.join(&platform))?;
-        out_file.write_all(serde_json::to_string_pretty(&repodata)?.as_bytes())?;
-        out_file.persist(output_folder.join(&platform).join("repodata.json"))?;
+    // If requested `target_platform` subdir does not exist, we create it.
+    if let Some(target_platform) = target_platform {
+        tracing::debug!("Did not find {target_platform} subdir, creating.");
+        if !subdirs.contains(&target_platform) {
+            op.create_dir(&format!("{}/", target_platform.as_str()))
+                .await?;
+        }
+        // Limit subdirs to only the requested `target_platform`.
+        subdirs = HashSet::default();
+        subdirs.insert(target_platform);
+    } else if !subdirs.contains(&Platform::NoArch) {
+        // If `noarch` subdir does not exist, we create it.
+        tracing::debug!("Did not find noarch subdir, creating.");
+        op.create_dir(&format!("{}/", Platform::NoArch.as_str()))
+            .await?;
+        subdirs.insert(Platform::NoArch);
     }
 
+    let multi_progress = MultiProgress::new();
+    let semaphore = Semaphore::new(max_parallel);
+    let semaphore = Arc::new(semaphore);
+
+    let tasks = subdirs
+        .iter()
+        .map(|subdir| {
+            tokio::spawn(index_subdir(
+                *subdir,
+                op.clone(),
+                force,
+                multi_progress.clone(),
+                semaphore.clone(),
+            ))
+        })
+        .collect::<Vec<_>>();
+    try_join_all(tasks).await?;
+
     Ok(())
 }
-
-// TODO: write proper unit tests for above functions
diff --git a/crates/rattler_index/src/main.rs b/crates/rattler_index/src/main.rs
new file mode 100644
index 000000000..dadb4601d
--- /dev/null
+++ b/crates/rattler_index/src/main.rs
@@ -0,0 +1,133 @@
+use clap::{arg, Parser, Subcommand};
+use clap_verbosity_flag::Verbosity;
+use rattler_conda_types::Platform;
+use rattler_index::{index_fs, index_s3};
+use tracing_log::AsTrace;
+use url::Url;
+
+fn parse_s3_url(value: &str) -> Result<Url, String> {
+    let url: Url = Url::parse(value).map_err(|e| format!("`{value}` isn't a valid URL: {e}"))?;
+    if url.scheme() == "s3" && url.host_str().is_some() {
+        Ok(url)
+    } else {
+        Err(format!(
+            "Only S3 URLs of format s3://bucket/... can be used, not `{value}`"
+        ))
+    }
+}
+
+/// The `rattler-index` CLI.
+#[derive(Parser)]
+#[command(version, about, long_about = None)]
+struct Cli {
+    #[command(subcommand)]
+    command: Commands,
+
+    #[command(flatten)]
+    verbose: Verbosity,
+
+    /// Whether to force the re-indexing of all packages.
+    /// Note that this will create a new repodata.json instead of updating the existing one.
+    #[arg(short, long, default_value = "false", global = true)]
+    force: bool,
+
+    /// The maximum number of packages to process in-memory simultaneously.
+    /// This is necessary to limit memory usage when indexing large channels.
+    #[arg(long, default_value = "128", global = true)]
+    max_parallel: usize,
+
+    /// A specific platform to index.
+    /// Defaults to all platforms available in the channel.
+    #[arg(long, global = true)]
+    target_platform: Option<Platform>,
+}
+
+/// The subcommands for the `rattler-index` CLI.
+#[derive(Subcommand)]
+#[allow(clippy::large_enum_variant)]
+enum Commands {
+    /// Index a channel stored on the filesystem.
+    #[command(name = "fs")]
+    FileSystem {
+        /// The path to the channel directory.
+        #[arg()]
+        channel: std::path::PathBuf,
+    },
+
+    /// Index a channel stored in an S3 bucket.
+    S3 {
+        /// The S3 channel URL, e.g. `s3://my-bucket/my-channel`.
+        #[arg(value_parser = parse_s3_url)]
+        channel: Url,
+
+        /// The endpoint URL of the S3 backend
+        #[arg(
+            long,
+            env = "S3_ENDPOINT_URL",
+            default_value = "https://s3.amazonaws.com"
+        )]
+        endpoint_url: Url,
+
+        /// The region of the S3 backend
+        #[arg(long, env = "S3_REGION", default_value = "eu-central-1")]
+        region: String,
+
+        /// Whether to use path-style S3 URLs
+        #[arg(long, env = "S3_FORCE_PATH_STYLE", default_value = "false")]
+        force_path_style: bool,
+
+        /// The access key ID for the S3 bucket.
+        #[arg(long, env = "S3_ACCESS_KEY_ID", requires_all = ["secret_access_key"])]
+        access_key_id: Option<String>,
+
+        /// The secret access key for the S3 bucket.
+        #[arg(long, env = "S3_SECRET_ACCESS_KEY", requires_all = ["access_key_id"])]
+        secret_access_key: Option<String>,
+
+        /// The session token for the S3 bucket.
+        #[arg(long, env = "S3_SESSION_TOKEN", requires_all = ["access_key_id", "secret_access_key"])]
+        session_token: Option<String>,
+    },
+}
+
+/// Entry point of the `rattler-index` cli.
+#[tokio::main]
+async fn main() -> anyhow::Result<()> {
+    // Parse the command line arguments
+    let cli = Cli::parse();
+
+    tracing_subscriber::FmtSubscriber::builder()
+        .with_max_level(cli.verbose.log_level_filter().as_trace())
+        .init();
+
+    match cli.command {
+        Commands::FileSystem { channel } => {
+            index_fs(channel, cli.target_platform, cli.force, cli.max_parallel).await
+        }
+        Commands::S3 {
+            channel,
+            region,
+            endpoint_url,
+            force_path_style,
+            access_key_id,
+            secret_access_key,
+            session_token,
+        } => {
+            index_s3(
+                channel,
+                region,
+                endpoint_url,
+                force_path_style,
+                access_key_id,
+                secret_access_key,
+                session_token,
+                cli.target_platform,
+                cli.force,
+                cli.max_parallel,
+            )
+            .await
+        }
+    }?;
+    println!("Finished indexing channel.");
+    Ok(())
+}
diff --git a/crates/rattler_index/tests/test_index.rs b/crates/rattler_index/tests/test_index.rs
index e789253ef..5fd83aeec 100644
--- a/crates/rattler_index/tests/test_index.rs
+++ b/crates/rattler_index/tests/test_index.rs
@@ -5,31 +5,39 @@ use std::{
 };
 
 use rattler_conda_types::Platform;
-use rattler_index::index;
+use rattler_index::index_fs;
 use serde_json::Value;
 
 fn test_data_dir() -> PathBuf {
     Path::new(env!("CARGO_MANIFEST_DIR")).join("../../test-data")
 }
 
-#[test]
-fn test_index() {
+#[tokio::test]
+async fn test_index() {
     let temp_dir = tempfile::tempdir().unwrap();
     let subdir_path = Path::new("win-64");
-    let conda_file_path = tools::download_and_cache_file(
-        "https://conda.anaconda.org/conda-forge/win-64/conda-22.11.1-py38haa244fe_1.conda"
-            .parse()
-            .unwrap(),
-        "a8a44c5ff2b2f423546d49721ba2e3e632233c74a813c944adf8e5742834930e",
-    )
+    let conda_file_path = tokio::task::spawn_blocking(|| {
+        tools::download_and_cache_file(
+            "https://conda.anaconda.org/conda-forge/win-64/conda-22.11.1-py38haa244fe_1.conda"
+                .parse()
+                .unwrap(),
+            "a8a44c5ff2b2f423546d49721ba2e3e632233c74a813c944adf8e5742834930e",
+        )
+    })
+    .await
+    .unwrap()
     .unwrap();
     let index_json_path = Path::new("conda-22.11.1-py38haa244fe_1-index.json");
-    let tar_bz2_file_path = tools::download_and_cache_file(
-        "https://conda.anaconda.org/conda-forge/win-64/conda-22.9.0-py38haa244fe_2.tar.bz2"
-            .parse()
-            .unwrap(),
-        "3c2c2e8e81bde5fb1ac4b014f51a62411feff004580c708c97a0ec2b7058cdc4",
-    )
+    let tar_bz2_file_path = tokio::task::spawn_blocking(|| {
+        tools::download_and_cache_file(
+            "https://conda.anaconda.org/conda-forge/win-64/conda-22.9.0-py38haa244fe_2.tar.bz2"
+                .parse()
+                .unwrap(),
+            "3c2c2e8e81bde5fb1ac4b014f51a62411feff004580c708c97a0ec2b7058cdc4",
+        )
+    })
+    .await
+    .unwrap()
     .unwrap();
 
     fs::create_dir(temp_dir.path().join(subdir_path)).unwrap();
@@ -50,7 +58,7 @@ fn test_index() {
     )
     .unwrap();
 
-    let res = index(temp_dir.path(), Some(&Platform::Win64));
+    let res = index_fs(temp_dir.path(), Some(Platform::Win64), true, 100).await;
     assert!(res.is_ok());
 
     let repodata_path = temp_dir.path().join(subdir_path).join("repodata.json");
@@ -84,10 +92,16 @@ fn test_index() {
     );
 }
 
-#[test]
-fn test_index_empty_directory() {
+#[tokio::test]
+async fn test_index_empty_directory_creates_noarch_repodata() {
     let temp_dir = tempfile::tempdir().unwrap();
-    let res = index(temp_dir.path(), None);
+    let noarch_path = temp_dir.path().join("noarch");
+    let repodata_path = noarch_path.join("repodata.json");
+
+    let res = index_fs(temp_dir.path(), None, true, 100).await;
+
     assert!(res.is_ok());
-    assert_eq!(fs::read_dir(temp_dir).unwrap().count(), 0);
+    assert!(noarch_path.is_dir());
+    assert_eq!(fs::read_dir(&noarch_path).unwrap().count(), 1);
+    assert!(repodata_path.is_file());
 }
diff --git a/crates/rattler_menuinst/src/macos.rs b/crates/rattler_menuinst/src/macos.rs
index 871b61172..c02ebdc6e 100644
--- a/crates/rattler_menuinst/src/macos.rs
+++ b/crates/rattler_menuinst/src/macos.rs
@@ -897,16 +897,16 @@ mod tests {
             for item in &parsed_schema.menu_items {
                 let icon = item.command.icon.as_ref().unwrap();
                 for ext in &["icns", "png", "svg"] {
-                    placeholders.insert("ICON_EXT".to_string(), ext.to_string());
+                    placeholders.insert("ICON_EXT".to_string(), (*ext).to_string());
                     let icon_path = icon.resolve(FakePlaceholders {
                         placeholders: placeholders.clone(),
                     });
-                    fs::write(&icon_path, &[]).unwrap();
+                    fs::write(&icon_path, []).unwrap();
                 }
             }
 
             fs::create_dir_all(prefix_path.join("bin")).unwrap();
-            fs::write(prefix_path.join("bin/python"), &[]).unwrap();
+            fs::write(prefix_path.join("bin/python"), []).unwrap();
 
             Self {
                 _tmp_dir: tmp_dir,
@@ -926,8 +926,8 @@ mod tests {
         let fake_prefix = FakePrefix::new(Path::new("spyder/menu.json"));
 
         let placeholders = super::BaseMenuItemPlaceholders::new(
-            &fake_prefix.prefix(),
-            &fake_prefix.prefix(),
+            fake_prefix.prefix(),
+            fake_prefix.prefix(),
             rattler_conda_types::Platform::current(),
         );
 
diff --git a/crates/rattler_package_streaming/Cargo.toml b/crates/rattler_package_streaming/Cargo.toml
index 34cbce506..c4baabd85 100644
--- a/crates/rattler_package_streaming/Cargo.toml
+++ b/crates/rattler_package_streaming/Cargo.toml
@@ -19,10 +19,15 @@ num_cpus = { workspace = true }
 rattler_conda_types = { path = "../rattler_conda_types", version = "0.31.0", default-features = false }
 rattler_digest = { path = "../rattler_digest", version = "1.0.6", default-features = false }
 rattler_networking = { path = "../rattler_networking", version = "0.22.5", default-features = false }
-rattler_redaction = { version = "0.1.6", path = "../rattler_redaction", features = ["reqwest", "reqwest-middleware"] }
+rattler_redaction = { version = "0.1.6", path = "../rattler_redaction", features = [
+  "reqwest",
+  "reqwest-middleware",
+], default-features = false }
 reqwest = { workspace = true, features = ["stream"], optional = true }
 reqwest-middleware = { workspace = true, optional = true }
-simple_spawn_blocking = { version = "1.1.0", path = "../simple_spawn_blocking", features = ["tokio"] }
+simple_spawn_blocking = { version = "1.1.0", path = "../simple_spawn_blocking", features = [
+  "tokio",
+] }
 serde_json = { workspace = true }
 tar = { workspace = true }
 tempfile = { workspace = true }
@@ -36,8 +41,8 @@ zstd = { workspace = true, features = ["zstdmt"] }
 
 [features]
 default = ["native-tls"]
-native-tls = ["rattler_networking/native-tls"]
-rustls-tls = ["rattler_networking/rustls-tls"]
+native-tls = ["rattler_networking/native-tls", "rattler_redaction/native-tls"]
+rustls-tls = ["rattler_networking/rustls-tls", "rattler_redaction/rustls-tls"]
 wasm = ["zstd/wasm"]
 reqwest = ["dep:reqwest-middleware", "dep:reqwest"]
 
diff --git a/crates/rattler_redaction/Cargo.toml b/crates/rattler_redaction/Cargo.toml
index 6bd07737f..9aad3e28c 100644
--- a/crates/rattler_redaction/Cargo.toml
+++ b/crates/rattler_redaction/Cargo.toml
@@ -10,7 +10,12 @@ repository.workspace = true
 license.workspace = true
 readme.workspace = true
 
+[features]
+default = ["rustls-tls"]
+native-tls = ["reqwest/native-tls", "reqwest/native-tls-alpn"]
+rustls-tls = ["reqwest/rustls-tls", "reqwest/rustls-tls-native-roots"]
+
 [dependencies]
 url = { workspace = true }
-reqwest = { workspace = true, optional = true }
+reqwest = { workspace = true, optional = true, default-features = false }
 reqwest-middleware = { workspace = true, optional = true }
diff --git a/crates/tools/Cargo.toml b/crates/tools/Cargo.toml
index ec27e53ed..548278d68 100644
--- a/crates/tools/Cargo.toml
+++ b/crates/tools/Cargo.toml
@@ -4,6 +4,11 @@ version = "0.1.0"
 edition = "2021"
 publish = false
 
+[features]
+default = ["rustls-tls"]
+native-tls = ["reqwest/native-tls"]
+rustls-tls = ["reqwest/rustls-tls"]
+
 [dependencies]
 anyhow = { workspace = true }
 bindgen = { workspace = true }
@@ -15,7 +20,9 @@ fslock = { workspace = true }
 dirs = { workspace = true }
 thiserror = { workspace = true }
 rattler_digest = { path = "../rattler_digest" }
-reqwest = { workspace = true, default-features = false, features = ["blocking", "rustls-tls"] }
+reqwest = { workspace = true, default-features = false, features = [
+  "blocking",
+] }
 tempfile = { workspace = true }
 tokio = { workspace = true }
 
diff --git a/py-rattler/pixi.lock b/py-rattler/pixi.lock
index f2ca53c19..b48ad7eba 100644
--- a/py-rattler/pixi.lock
+++ b/py-rattler/pixi.lock
@@ -885,7 +885,14 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/linux-64/xz-5.2.6-h166bdaf_0.tar.bz2
       - conda: https://conda.anaconda.org/conda-forge/linux-64/zstandard-0.23.0-py39h08a7858_1.conda
       - conda: https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.6-ha6fb4c9_0.conda
+      - pypi: https://files.pythonhosted.org/packages/ac/6e/faf7c6c3ae59641c75023fb5dcc8a02c33752ac8ccadf9931e8d8364f2fe/boto3-1.7.84-py2.py3-none-any.whl
+      - pypi: https://files.pythonhosted.org/packages/01/b7/cb08cd1af2bb0d0dfb393101a93b6ab6fb80f109ab7b37f2f34386c11351/botocore-1.10.84-py2.py3-none-any.whl
+      - pypi: https://files.pythonhosted.org/packages/8f/d7/9322c609343d929e75e7e5e6255e614fcc67572cfd083959cdef3b7aad79/docutils-0.21.2-py3-none-any.whl
+      - pypi: https://files.pythonhosted.org/packages/07/cb/5f001272b6faeb23c1c9e0acc04d48eaaf5c862c17709d20e3469c6e0139/jmespath-0.10.0-py2.py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/7a/7c/d7b2a0417af6428440c0ad7cb9799073e507b1a465f827d058b826236964/numpy-1.24.4-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
+      - pypi: https://files.pythonhosted.org/packages/ec/57/56b9bcc3c9c6a792fcbaf139543cee77261f3651ca9da0c93f5c1221264b/python_dateutil-2.9.0.post0-py2.py3-none-any.whl
+      - pypi: https://files.pythonhosted.org/packages/d7/14/2a0004d487464d120c9fb85313a75cd3d71a7506955be458eebfe19a6b1d/s3transfer-0.1.13-py2.py3-none-any.whl
+      - pypi: https://files.pythonhosted.org/packages/b7/ce/149a00dd41f10bc29e5921b496af8b574d8413afcd5e30dfa0ed46c2cc5e/six-1.17.0-py2.py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/c4/83/07c5cd92ead27ecf48e3d12d0164ac0f6a7990b4d0d47c297398c285627a/types_networkx-3.3.0.20241020-py3-none-any.whl
       osx-64:
       - conda: https://conda.anaconda.org/conda-forge/osx-64/brotli-python-1.1.0-py39h7c0e7c0_2.conda
@@ -946,7 +953,14 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/osx-64/xz-5.2.6-h775f41a_0.tar.bz2
       - conda: https://conda.anaconda.org/conda-forge/osx-64/zstandard-0.23.0-py39hc23f734_1.conda
       - conda: https://conda.anaconda.org/conda-forge/osx-64/zstd-1.5.6-h915ae27_0.conda
+      - pypi: https://files.pythonhosted.org/packages/ac/6e/faf7c6c3ae59641c75023fb5dcc8a02c33752ac8ccadf9931e8d8364f2fe/boto3-1.7.84-py2.py3-none-any.whl
+      - pypi: https://files.pythonhosted.org/packages/01/b7/cb08cd1af2bb0d0dfb393101a93b6ab6fb80f109ab7b37f2f34386c11351/botocore-1.10.84-py2.py3-none-any.whl
+      - pypi: https://files.pythonhosted.org/packages/8f/d7/9322c609343d929e75e7e5e6255e614fcc67572cfd083959cdef3b7aad79/docutils-0.21.2-py3-none-any.whl
+      - pypi: https://files.pythonhosted.org/packages/07/cb/5f001272b6faeb23c1c9e0acc04d48eaaf5c862c17709d20e3469c6e0139/jmespath-0.10.0-py2.py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/9a/cd/d5b0402b801c8a8b56b04c1e85c6165efab298d2f0ab741c2406516ede3a/numpy-1.24.4-cp39-cp39-macosx_10_9_x86_64.whl
+      - pypi: https://files.pythonhosted.org/packages/ec/57/56b9bcc3c9c6a792fcbaf139543cee77261f3651ca9da0c93f5c1221264b/python_dateutil-2.9.0.post0-py2.py3-none-any.whl
+      - pypi: https://files.pythonhosted.org/packages/d7/14/2a0004d487464d120c9fb85313a75cd3d71a7506955be458eebfe19a6b1d/s3transfer-0.1.13-py2.py3-none-any.whl
+      - pypi: https://files.pythonhosted.org/packages/b7/ce/149a00dd41f10bc29e5921b496af8b574d8413afcd5e30dfa0ed46c2cc5e/six-1.17.0-py2.py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/c4/83/07c5cd92ead27ecf48e3d12d0164ac0f6a7990b4d0d47c297398c285627a/types_networkx-3.3.0.20241020-py3-none-any.whl
       osx-arm64:
       - conda: https://conda.anaconda.org/conda-forge/osx-arm64/brotli-python-1.1.0-py39hfa9831e_2.conda
@@ -1007,7 +1021,14 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/osx-arm64/xz-5.2.6-h57fd34a_0.tar.bz2
       - conda: https://conda.anaconda.org/conda-forge/osx-arm64/zstandard-0.23.0-py39hcf1bb16_1.conda
       - conda: https://conda.anaconda.org/conda-forge/osx-arm64/zstd-1.5.6-hb46c0d2_0.conda
+      - pypi: https://files.pythonhosted.org/packages/ac/6e/faf7c6c3ae59641c75023fb5dcc8a02c33752ac8ccadf9931e8d8364f2fe/boto3-1.7.84-py2.py3-none-any.whl
+      - pypi: https://files.pythonhosted.org/packages/01/b7/cb08cd1af2bb0d0dfb393101a93b6ab6fb80f109ab7b37f2f34386c11351/botocore-1.10.84-py2.py3-none-any.whl
+      - pypi: https://files.pythonhosted.org/packages/8f/d7/9322c609343d929e75e7e5e6255e614fcc67572cfd083959cdef3b7aad79/docutils-0.21.2-py3-none-any.whl
+      - pypi: https://files.pythonhosted.org/packages/07/cb/5f001272b6faeb23c1c9e0acc04d48eaaf5c862c17709d20e3469c6e0139/jmespath-0.10.0-py2.py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/14/27/638aaa446f39113a3ed38b37a66243e21b38110d021bfcb940c383e120f2/numpy-1.24.4-cp39-cp39-macosx_11_0_arm64.whl
+      - pypi: https://files.pythonhosted.org/packages/ec/57/56b9bcc3c9c6a792fcbaf139543cee77261f3651ca9da0c93f5c1221264b/python_dateutil-2.9.0.post0-py2.py3-none-any.whl
+      - pypi: https://files.pythonhosted.org/packages/d7/14/2a0004d487464d120c9fb85313a75cd3d71a7506955be458eebfe19a6b1d/s3transfer-0.1.13-py2.py3-none-any.whl
+      - pypi: https://files.pythonhosted.org/packages/b7/ce/149a00dd41f10bc29e5921b496af8b574d8413afcd5e30dfa0ed46c2cc5e/six-1.17.0-py2.py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/c4/83/07c5cd92ead27ecf48e3d12d0164ac0f6a7990b4d0d47c297398c285627a/types_networkx-3.3.0.20241020-py3-none-any.whl
       win-64:
       - conda: https://conda.anaconda.org/conda-forge/win-64/brotli-python-1.1.0-py39ha51f57c_2.conda
@@ -1076,7 +1097,14 @@ environments:
       - conda: https://conda.anaconda.org/conda-forge/win-64/xz-5.2.6-h8d14728_0.tar.bz2
       - conda: https://conda.anaconda.org/conda-forge/win-64/zstandard-0.23.0-py39h9bf74da_1.conda
       - conda: https://conda.anaconda.org/conda-forge/win-64/zstd-1.5.6-h0ea2cb4_0.conda
+      - pypi: https://files.pythonhosted.org/packages/ac/6e/faf7c6c3ae59641c75023fb5dcc8a02c33752ac8ccadf9931e8d8364f2fe/boto3-1.7.84-py2.py3-none-any.whl
+      - pypi: https://files.pythonhosted.org/packages/01/b7/cb08cd1af2bb0d0dfb393101a93b6ab6fb80f109ab7b37f2f34386c11351/botocore-1.10.84-py2.py3-none-any.whl
+      - pypi: https://files.pythonhosted.org/packages/8f/d7/9322c609343d929e75e7e5e6255e614fcc67572cfd083959cdef3b7aad79/docutils-0.21.2-py3-none-any.whl
+      - pypi: https://files.pythonhosted.org/packages/07/cb/5f001272b6faeb23c1c9e0acc04d48eaaf5c862c17709d20e3469c6e0139/jmespath-0.10.0-py2.py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/63/38/6cc19d6b8bfa1d1a459daf2b3fe325453153ca7019976274b6f33d8b5663/numpy-1.24.4-cp39-cp39-win_amd64.whl
+      - pypi: https://files.pythonhosted.org/packages/ec/57/56b9bcc3c9c6a792fcbaf139543cee77261f3651ca9da0c93f5c1221264b/python_dateutil-2.9.0.post0-py2.py3-none-any.whl
+      - pypi: https://files.pythonhosted.org/packages/d7/14/2a0004d487464d120c9fb85313a75cd3d71a7506955be458eebfe19a6b1d/s3transfer-0.1.13-py2.py3-none-any.whl
+      - pypi: https://files.pythonhosted.org/packages/b7/ce/149a00dd41f10bc29e5921b496af8b574d8413afcd5e30dfa0ed46c2cc5e/six-1.17.0-py2.py3-none-any.whl
       - pypi: https://files.pythonhosted.org/packages/c4/83/07c5cd92ead27ecf48e3d12d0164ac0f6a7990b4d0d47c297398c285627a/types_networkx-3.3.0.20241020-py3-none-any.whl
 packages:
 - conda: https://conda.anaconda.org/conda-forge/linux-64/_libgcc_mutex-0.1-conda_forge.tar.bz2
@@ -1145,6 +1173,25 @@ packages:
   purls: []
   size: 5682777
   timestamp: 1729655371045
+- pypi: https://files.pythonhosted.org/packages/ac/6e/faf7c6c3ae59641c75023fb5dcc8a02c33752ac8ccadf9931e8d8364f2fe/boto3-1.7.84-py2.py3-none-any.whl
+  name: boto3
+  version: 1.7.84
+  sha256: 0ed4b107c3b4550547aaec3c9bb17df068ff92d1f6f4781205800e2cb8a66de5
+  requires_dist:
+  - botocore>=1.10.84,<1.11.0
+  - jmespath>=0.7.1,<1.0.0
+  - s3transfer>=0.1.10,<0.2.0
+- pypi: https://files.pythonhosted.org/packages/01/b7/cb08cd1af2bb0d0dfb393101a93b6ab6fb80f109ab7b37f2f34386c11351/botocore-1.10.84-py2.py3-none-any.whl
+  name: botocore
+  version: 1.10.84
+  sha256: 380852e1adb9ba4ba9ff096af61f88a6888197b86e580e1bd786f04ebe6f9c0c
+  requires_dist:
+  - python-dateutil>=2.1,<2.7.0 ; python_full_version == '2.6.*'
+  - python-dateutil>=2.1,<3.0.0 ; python_full_version >= '2.7'
+  - jmespath>=0.7.1,<1.0.0
+  - docutils>=0.10
+  - ordereddict==1.1 ; python_full_version == '2.6.*'
+  - simplejson==3.3.0 ; python_full_version == '2.6.*'
 - conda: https://conda.anaconda.org/conda-forge/linux-64/brotli-python-1.1.0-py312h2ec8cdc_2.conda
   sha256: f2a59ccd20b4816dea9a2a5cb917eb69728271dbf1aeab4e1b7e609330a50b6f
   md5: b0b867af6fc74b2a0aa206da29c0f3cf
@@ -1679,6 +1726,11 @@ packages:
   license_family: PSF
   size: 24062
   timestamp: 1615232388757
+- pypi: https://files.pythonhosted.org/packages/8f/d7/9322c609343d929e75e7e5e6255e614fcc67572cfd083959cdef3b7aad79/docutils-0.21.2-py3-none-any.whl
+  name: docutils
+  version: 0.21.2
+  sha256: dafca5b9e384f0e419294eb4d2ff9fa826435bf15f15b7bd45723e8ad76811b2
+  requires_python: '>=3.9'
 - conda: https://conda.anaconda.org/conda-forge/noarch/exceptiongroup-1.2.2-pyhd8ed1ab_0.conda
   sha256: e0edd30c4b7144406bb4da975e6bb97d6bc9c0e999aa4efe66ae108cada5d5b5
   md5: d02ae936e42063ca46af6cdad2dbd1e0
@@ -2096,6 +2148,11 @@ packages:
   license_family: BSD
   size: 111565
   timestamp: 1715127275924
+- pypi: https://files.pythonhosted.org/packages/07/cb/5f001272b6faeb23c1c9e0acc04d48eaaf5c862c17709d20e3469c6e0139/jmespath-0.10.0-py2.py3-none-any.whl
+  name: jmespath
+  version: 0.10.0
+  sha256: cdf6525904cc597730141d61b36f2e4b8ecc257c420fa2f4549bac2c2d0cb72f
+  requires_python: '>=2.6,!=3.0.*,!=3.1.*,!=3.2.*'
 - conda: https://conda.anaconda.org/conda-forge/noarch/kernel-headers_linux-64-3.10.0-he073ed8_17.conda
   sha256: c28d69ca84533f0e2093f17ae6d3e19ee3661dd397618630830b1b9afc3bfb4d
   md5: 285931bd28b3b8f176d46dd9fd627a09
@@ -4389,6 +4446,13 @@ packages:
   purls: []
   size: 17024927
   timestamp: 1727718943163
+- pypi: https://files.pythonhosted.org/packages/ec/57/56b9bcc3c9c6a792fcbaf139543cee77261f3651ca9da0c93f5c1221264b/python_dateutil-2.9.0.post0-py2.py3-none-any.whl
+  name: python-dateutil
+  version: 2.9.0.post0
+  sha256: a8b2bc7bffae282281c8140a97d3aa9c14da0b136dfe83f850eea9a5f7470427
+  requires_dist:
+  - six>=1.5
+  requires_python: '>=2.7,!=3.0.*,!=3.1.*,!=3.2.*'
 - conda: https://conda.anaconda.org/conda-forge/noarch/python-dateutil-2.9.0-pyhd8ed1ab_0.conda
   sha256: f3ceef02ac164a8d3a080d0d32f8e2ebe10dd29e3a685d240e38b3599e146320
   md5: 2cf4264fffb9e6eff6031c5b6884d61c
@@ -4884,6 +4948,13 @@ packages:
   purls: []
   size: 36747126
   timestamp: 1740489714324
+- pypi: https://files.pythonhosted.org/packages/d7/14/2a0004d487464d120c9fb85313a75cd3d71a7506955be458eebfe19a6b1d/s3transfer-0.1.13-py2.py3-none-any.whl
+  name: s3transfer
+  version: 0.1.13
+  sha256: c7a9ec356982d5e9ab2d4b46391a7d6a950e2b04c472419f5fdec70cc0ada72f
+  requires_dist:
+  - botocore>=1.3.0,<2.0.0
+  - futures>=2.2.0,<4.0.0 ; python_full_version >= '2.6' and python_full_version < '2.8'
 - conda: https://conda.anaconda.org/conda-forge/noarch/setuptools-75.1.0-pyhd8ed1ab_0.conda
   sha256: 6725235722095c547edd24275053c615158d6163f396550840aebd6e209e4738
   md5: d5cd48392c67fb6849ba459c2c2b671f
@@ -4906,6 +4977,11 @@ packages:
   - pkg:pypi/shellingham?source=hash-mapping
   size: 14568
   timestamp: 1698144516278
+- pypi: https://files.pythonhosted.org/packages/b7/ce/149a00dd41f10bc29e5921b496af8b574d8413afcd5e30dfa0ed46c2cc5e/six-1.17.0-py2.py3-none-any.whl
+  name: six
+  version: 1.17.0
+  sha256: 4721f391ed90541fddacab5acf947aa0d3dc7d27b2e1e8eda2be8970586c3274
+  requires_python: '>=2.7,!=3.0.*,!=3.1.*,!=3.2.*'
 - conda: https://conda.anaconda.org/conda-forge/noarch/six-1.16.0-pyh6c4a22f_0.tar.bz2
   sha256: a85c38227b446f42c5b90d9b642f2c0567880c15d72492d8da074a59c8f91dd6
   md5: e5f25f8dbc060e9a8d912e432202afc2
diff --git a/py-rattler/pixi.toml b/py-rattler/pixi.toml
index e5020de92..1b92812df 100644
--- a/py-rattler/pixi.toml
+++ b/py-rattler/pixi.toml
@@ -2,8 +2,8 @@
 name = "py-rattler"
 description = "Add a short description here"
 authors = [
-    "Bas Zalmstra <bas@prefix.dev>",
-    "Tarun Pratap Singh <pratapsinghtarun9@gmail.com>",
+  "Bas Zalmstra <bas@prefix.dev>",
+  "Tarun Pratap Singh <pratapsinghtarun9@gmail.com>",
 ]
 channels = ["conda-forge"]
 platforms = ["win-64", "linux-64", "osx-64", "osx-arm64"]
@@ -39,6 +39,8 @@ typer = "*"
 
 [feature.test.pypi-dependencies]
 types-networkx = "*"
+# boto3 on conda-forge requires python >=3.10
+boto3 = "*"
 
 [feature.test.tasks]
 test = { cmd = "pytest --doctest-modules", depends-on = ["build"] }
diff --git a/py-rattler/rattler/index/__init__.py b/py-rattler/rattler/index/__init__.py
index 9023b5dd1..060834cbb 100644
--- a/py-rattler/rattler/index/__init__.py
+++ b/py-rattler/rattler/index/__init__.py
@@ -1,3 +1,3 @@
-from rattler.index.index import index
+from rattler.index.index import index_fs, index_s3
 
-__all__ = ["index"]
+__all__ = ["index_s3", "index_fs"]
diff --git a/py-rattler/rattler/index/index.py b/py-rattler/rattler/index/index.py
index a55cce8e8..f8c716508 100644
--- a/py-rattler/rattler/index/index.py
+++ b/py-rattler/rattler/index/index.py
@@ -1,14 +1,17 @@
 from __future__ import annotations
+
 import os
 from typing import Optional
 
 from rattler.platform import Platform
-from rattler.rattler import py_index
+from rattler.rattler import py_index_fs, py_index_s3
 
 
-def index(
+async def index_fs(
     channel_directory: os.PathLike[str],
     target_platform: Optional[Platform] = None,
+    force: bool = False,
+    max_parallel: int = 128,
 ) -> None:
     """
     Indexes dependencies in the `channel_directory` for one or more subdirectories within said directory.
@@ -21,8 +24,58 @@ def index(
         channel_directory: A `os.PathLike[str]` that is the directory containing subdirectories
                            of dependencies to index.
         target_platform(optional): A `Platform` to index dependencies for.
+        force: Whether to forcefully re-index all subdirs.
+        max_parallel: The maximum number of packages to process in-memory simultaneously.
     """
-    py_index(
+    await py_index_fs(
         channel_directory,
         target_platform._inner if target_platform else target_platform,
+        force,
+        max_parallel,
+    )
+
+
+async def index_s3(
+    channel_url: str,
+    region: str,
+    endpoint_url: str,
+    force_path_style: bool = False,
+    access_key_id: Optional[str] = None,
+    secret_access_key: Optional[str] = None,
+    session_token: Optional[str] = None,
+    target_platform: Optional[Platform] = None,
+    force: bool = False,
+    max_parallel: int = 128,
+) -> None:
+    """
+    Indexes dependencies in the `channel_url` for one or more subdirectories in the S3 directory.
+    Will generate repodata.json files in each subdirectory containing metadata about each present package,
+    or if `target_platform` is specified will only consider the subdirectory corresponding to this platform.
+    Will always index the "noarch" subdirectory, and thus this subdirectory should always be present, because
+    conda channels at a minimum must include this subdirectory.
+
+    Arguments:
+        channel_url: An S3 URL (e.g., s3://my-bucket/my-channel that containins the subdirectories
+                     of dependencies to index.
+        region: The region of the S3 bucket.
+        endpoint_url: The endpoint URL of the S3 bucket.
+        force_path_style: Whether to use path-style addressing for S3.
+        access_key_id(optional): The access key ID to use for authentication.
+        secret_access_key(optional): The secret access key to use for authentication.
+        session_token(optional): The session token to use for authentication.
+        target_platform(optional): A `Platform` to index dependencies for.
+        force: Whether to forcefully re-index all subdirs.
+        max_parallel: The maximum number of packages to process in-memory simultaneously.
+    """
+    await py_index_s3(
+        channel_url,
+        region,
+        endpoint_url,
+        force_path_style,
+        access_key_id,
+        secret_access_key,
+        session_token,
+        target_platform._inner if target_platform else target_platform,
+        force,
+        max_parallel,
     )
diff --git a/py-rattler/src/index.rs b/py-rattler/src/index.rs
index 17a04c4a3..5658441f9 100644
--- a/py-rattler/src/index.rs
+++ b/py-rattler/src/index.rs
@@ -1,23 +1,63 @@
-use pyo3::{pyfunction, PyResult, Python};
+use pyo3::{pyfunction, Bound, PyAny, PyResult, Python};
+use pyo3_async_runtimes::tokio::future_into_py;
 use rattler_conda_types::Platform;
-use rattler_index::index;
+use rattler_index::{index_fs, index_s3};
+use url::Url;
 
 use std::path::PathBuf;
 
 use crate::{error::PyRattlerError, platform::PyPlatform};
 
 #[pyfunction]
-#[pyo3(signature = (channel_directory, target_platform=None))]
-pub fn py_index(
+#[pyo3(signature = (channel_directory, target_platform=None, force=false, max_parallel=128))]
+pub fn py_index_fs(
     py: Python<'_>,
     channel_directory: PathBuf,
     target_platform: Option<PyPlatform>,
-) -> PyResult<()> {
-    py.allow_threads(move || {
-        let path = channel_directory.as_path();
-        match index(path, target_platform.map(Platform::from).as_ref()) {
-            Ok(_v) => Ok(()),
-            Err(e) => Err(PyRattlerError::from(e).into()),
-        }
+    force: bool,
+    max_parallel: usize,
+) -> PyResult<Bound<'_, PyAny>> {
+    future_into_py(py, async move {
+        let target_platform = target_platform.map(Platform::from);
+        index_fs(channel_directory, target_platform, force, max_parallel)
+            .await
+            .map_err(|e| PyRattlerError::from(e).into())
+    })
+}
+
+#[pyfunction]
+#[allow(clippy::too_many_arguments)]
+#[pyo3(signature = (channel_url, region, endpoint_url, force_path_style, access_key_id=None,secret_access_key=None, session_token=None, target_platform=None, force=false, max_parallel=128))]
+pub fn py_index_s3(
+    py: Python<'_>,
+    channel_url: String,
+    region: String,
+    endpoint_url: String,
+    force_path_style: bool,
+    access_key_id: Option<String>,
+    secret_access_key: Option<String>,
+    session_token: Option<String>,
+    target_platform: Option<PyPlatform>,
+    force: bool,
+    max_parallel: usize,
+) -> PyResult<Bound<'_, PyAny>> {
+    let channel_url = Url::parse(&channel_url).map_err(PyRattlerError::from)?;
+    let endpoint_url = Url::parse(&endpoint_url).map_err(PyRattlerError::from)?;
+    let target_platform = target_platform.map(Platform::from);
+    future_into_py(py, async move {
+        index_s3(
+            channel_url,
+            region,
+            endpoint_url,
+            force_path_style,
+            access_key_id,
+            secret_access_key,
+            session_token,
+            target_platform,
+            force,
+            max_parallel,
+        )
+        .await
+        .map_err(|e| PyRattlerError::from(e).into())
     })
 }
diff --git a/py-rattler/src/lib.rs b/py-rattler/src/lib.rs
index 0416ec35a..fb25ea572 100644
--- a/py-rattler/src/lib.rs
+++ b/py-rattler/src/lib.rs
@@ -41,7 +41,7 @@ use error::{
 };
 use explicit_environment_spec::{PyExplicitEnvironmentEntry, PyExplicitEnvironmentSpec};
 use generic_virtual_package::PyGenericVirtualPackage;
-use index::py_index;
+use index::{py_index_fs, py_index_s3};
 use index_json::PyIndexJson;
 use installer::py_install;
 use lock::{
@@ -160,7 +160,8 @@ fn rattler<'py>(py: Python<'py>, m: Bound<'py, PyModule>) -> PyResult<()> {
     m.add_function(wrap_pyfunction!(py_solve_with_sparse_repodata, &m).unwrap())?;
     m.add_function(wrap_pyfunction!(get_rattler_version, &m).unwrap())?;
     m.add_function(wrap_pyfunction!(py_install, &m).unwrap())?;
-    m.add_function(wrap_pyfunction!(py_index, &m).unwrap())?;
+    m.add_function(wrap_pyfunction!(py_index_fs, &m).unwrap())?;
+    m.add_function(wrap_pyfunction!(py_index_s3, &m).unwrap())?;
 
     m.add_function(wrap_pyfunction!(package_streaming::extract_tar_bz2, &m).unwrap())?;
     m.add_function(wrap_pyfunction!(package_streaming::extract, &m).unwrap())?;
diff --git a/py-rattler/tests/unit/test_index.py b/py-rattler/tests/unit/test_index.py
index f79bc6c1d..c8e894982 100644
--- a/py-rattler/tests/unit/test_index.py
+++ b/py-rattler/tests/unit/test_index.py
@@ -1,10 +1,18 @@
 # type: ignore
 import os
+import shutil
+import uuid
+from dataclasses import dataclass, field
 from pathlib import Path
+from typing import Iterator
+
+import boto3
 import pytest
-import shutil
 
-from rattler import Platform, index
+from rattler import Platform
+from rattler.index import index_fs, index_s3
+
+# ------------------------------------ FILESYSTEM ------------------------------------ #
 
 
 @pytest.fixture
@@ -18,8 +26,9 @@ def package_directory(tmp_path, package_file_ruff: Path, package_file_pytweening
     return tmp_path
 
 
-def test_index(package_directory):
-    index(package_directory)
+@pytest.mark.asyncio
+async def test_index(package_directory):
+    await index_fs(package_directory)
 
     assert set(os.listdir(package_directory)) == {"noarch", "win-64"}
     assert "repodata.json" in os.listdir(package_directory / "win-64")
@@ -30,19 +39,18 @@ def test_index(package_directory):
         assert "pytweening-1.0.4-pyhd8ed1ab_0" in f.read()
 
 
-def test_index_specific_subdir_non_noarch(package_directory):
-    index(package_directory, Platform("win-64"))
+@pytest.mark.asyncio
+async def test_index_specific_subdir_non_noarch(package_directory):
+    await index_fs(package_directory, Platform("win-64"))
 
     assert "repodata.json" in os.listdir(package_directory / "win-64")
     with open(package_directory / "win-64/repodata.json") as f:
         assert "ruff-0.0.171-py310h298983d_0" in f.read()
-    assert "repodata.json" in os.listdir(package_directory / "noarch")
-    with open(package_directory / "noarch/repodata.json") as f:
-        assert "pytweening-1.0.4-pyhd8ed1ab_0" in f.read()
 
 
-def test_index_specific_subdir_noarch(package_directory):
-    index(package_directory, Platform("noarch"))
+@pytest.mark.asyncio
+async def test_index_specific_subdir_noarch(package_directory):
+    await index_fs(package_directory, Platform("noarch"))
 
     win_files = os.listdir(package_directory / "win-64")
     assert "repodata.json" not in win_files
@@ -50,3 +58,90 @@ def test_index_specific_subdir_noarch(package_directory):
     assert "repodata.json" in os.listdir(package_directory / "noarch")
     with open(package_directory / "noarch/repodata.json") as f:
         assert "pytweening-1.0.4-pyhd8ed1ab_0" in f.read()
+
+
+# ---------------------------------------- S3 ---------------------------------------- #
+
+
+@dataclass
+class S3Config:
+    access_key_id: str
+    secret_access_key: str
+    region: str = "auto"
+    endpoint_url: str = "https://e1a7cde76f1780ec06bac859036dbaf7.r2.cloudflarestorage.com"
+    bucket_name: str = "rattler-build-upload-test"
+    channel_name: str = field(default_factory=lambda: f"channel{uuid.uuid4()}")
+
+
+@pytest.fixture()
+def s3_config() -> S3Config:
+    access_key_id = os.environ.get("RATTLER_TEST_R2_ACCESS_KEY_ID")
+    if not access_key_id:
+        pytest.skip("RATTLER_TEST_R2_ACCESS_KEY_ID environment variable is not set")
+    secret_access_key = os.environ.get("RATTLER_TEST_R2_SECRET_ACCESS_KEY")
+    if not secret_access_key:
+        pytest.skip("RATTLER_TEST_R2_SECRET_ACCESS_KEY environment variable is not set")
+    return S3Config(
+        access_key_id=access_key_id,
+        secret_access_key=secret_access_key,
+    )
+
+
+@pytest.fixture()
+def s3_client(s3_config: S3Config):
+    return boto3.client(
+        service_name="s3",
+        endpoint_url=s3_config.endpoint_url,
+        aws_access_key_id=s3_config.access_key_id,
+        aws_secret_access_key=s3_config.secret_access_key,
+        region_name=s3_config.region,
+    )
+
+
+@pytest.fixture()
+def s3_channel(s3_config: S3Config, s3_client) -> Iterator[str]:
+    channel_url = f"s3://{s3_config.bucket_name}/{s3_config.channel_name}"
+
+    yield channel_url
+
+    # Clean up the channel after the test
+    objects_to_delete = s3_client.list_objects_v2(Bucket=s3_config.bucket_name, Prefix=f"{s3_config.channel_name}/")
+    delete_keys = [{"Key": obj["Key"]} for obj in objects_to_delete.get("Contents", [])]
+    if delete_keys:
+        result = s3_client.delete_objects(Bucket=s3_config.bucket_name, Delete={"Objects": delete_keys})
+        assert result["ResponseMetadata"]["HTTPStatusCode"] == 200
+
+
+@pytest.mark.asyncio
+async def test_index_s3(
+    package_directory,
+    s3_config: S3Config,
+    s3_channel: str,
+    s3_client,
+):
+    # Upload package to channel
+    filepath = package_directory / "noarch" / "pytweening-1.0.4-pyhd8ed1ab_0.tar.bz2"
+    s3_client.upload_file(
+        Filename=str(filepath),
+        Bucket=s3_config.bucket_name,
+        Key=f"{s3_config.channel_name}/noarch/pytweening-1.0.4-pyhd8ed1ab_0.tar.bz2",
+    )
+
+    # Run index command
+    await index_s3(
+        channel_url=s3_channel,
+        region=s3_config.region,
+        endpoint_url=s3_config.endpoint_url,
+        force_path_style=True,
+        access_key_id=s3_config.access_key_id,
+        secret_access_key=s3_config.secret_access_key,
+        force=True,
+    )
+
+    # Check if repodata.json was created
+    repodata_json = f"{s3_config.channel_name}/noarch/repodata.json"
+    result = s3_client.head_object(
+        Bucket=s3_config.bucket_name,
+        Key=repodata_json,
+    )
+    assert result["ResponseMetadata"]["HTTPStatusCode"] == 200