diff --git a/ci/install-upstream-wheels.sh b/ci/install-upstream-wheels.sh
index af4b68b0d9b..fc19516f480 100755
--- a/ci/install-upstream-wheels.sh
+++ b/ci/install-upstream-wheels.sh
@@ -1,7 +1,5 @@
 #!/usr/bin/env bash
 
-# install cython for building cftime without build isolation
-micromamba install "cython>=0.29.20" py-cpuinfo setuptools-scm
 # temporarily (?) remove numbagg and numba
 micromamba remove -y numba numbagg sparse
 # temporarily remove numexpr
@@ -18,10 +16,9 @@ micromamba remove -y --force \
     zarr \
     cftime \
     packaging \
-    pint \
     bottleneck \
-    flox \
-    numcodecs
+    flox
+    # pint
 # to limit the runtime of Upstream CI
 python -m pip install \
     -i https://pypi.anaconda.org/scientific-python-nightly-wheels/simple \
@@ -42,23 +39,6 @@ python -m pip install \
     --pre \
     --upgrade \
     pyarrow
-# without build isolation for packages compiling against numpy
-# TODO: remove once there are `numpy>=2.0` builds for these
-python -m pip install \
-    --no-deps \
-    --upgrade \
-    --no-build-isolation \
-    git+https://github.com/Unidata/cftime
-python -m pip install \
-    --no-deps \
-    --upgrade \
-    --no-build-isolation \
-    git+https://github.com/zarr-developers/numcodecs
-python -m pip install \
-    --no-deps \
-    --upgrade \
-    --no-build-isolation \
-    git+https://github.com/pydata/bottleneck
 python -m pip install \
     --no-deps \
     --upgrade \
@@ -66,8 +46,10 @@ python -m pip install \
     git+https://github.com/dask/dask-expr \
     git+https://github.com/dask/distributed \
     git+https://github.com/zarr-developers/zarr \
+    git+https://github.com/Unidata/cftime \
     git+https://github.com/pypa/packaging \
     git+https://github.com/hgrecco/pint \
+    git+https://github.com/pydata/bottleneck \
     git+https://github.com/intake/filesystem_spec \
     git+https://github.com/SciTools/nc-time-axis \
     git+https://github.com/xarray-contrib/flox \