diff --git a/.github/workflows/big-endian.yml b/.github/workflows/big-endian.yml
index 0119f04ffa..7bf78eacf5 100644
--- a/.github/workflows/big-endian.yml
+++ b/.github/workflows/big-endian.yml
@@ -57,7 +57,10 @@ jobs:
         run: |
           docker run --rm --platform linux/s390x -v "$PWD":/src:ro zarr-big-endian bash -euc '
             cp -r /src /work && cd /work
-            pip install -q --no-deps --no-build-isolation .
+            # Resolve dependencies against pyproject.toml rather than trusting whatever the
+            # image provides, then fail if any installed package falls outside the constraints.
+            pip install -q --no-build-isolation .
+            pip check
             python -c "import sys; assert sys.byteorder == \"big\", sys.byteorder"
             python -m pytest -p no:cacheprovider --hypothesis-profile ci -n auto \
               tests/test_dtype tests/test_dtype_registry.py \
diff --git a/changes/4547.misc.md b/changes/4547.misc.md
new file mode 100644
index 0000000000..f98644f479
--- /dev/null
+++ b/changes/4547.misc.md
@@ -0,0 +1 @@
+The big-endian (s390x) CI job now installs zarr with its dependencies resolved against `pyproject.toml` and runs `pip check`, instead of trusting whatever versions the Debian-based test image provides. The image builds a numcodecs that satisfies zarr's constraints from source where Debian's package does not.
diff --git a/ci/big-endian/Dockerfile b/ci/big-endian/Dockerfile
index 973ce698be..8c70535fc7 100644
--- a/ci/big-endian/Dockerfile
+++ b/ci/big-endian/Dockerfile
@@ -1,11 +1,20 @@
 # Test image for a big-endian host (s390x, run under QEMU by .github/workflows/big-endian.yml).
-# Debian packages supply numpy and numcodecs, so nothing heavy compiles under emulation;
-# this is also the environment Debian tests zarr in. Debian does not package Google's
-# crc32c library, so it is built here for the google-crc32c C extension.
+#
+# Debian packages are used as a source of prebuilt binaries for s390x, which PyPI does not
+# have, so that numpy and friends do not compile under emulation. They do not define the
+# test environment: zarr's pyproject.toml does. The workflow installs zarr with its
+# dependencies resolved and runs `pip check`, so a Debian package that falls outside the
+# declared constraints fails the job at install time instead of through unrelated-looking
+# test failures. Anything Debian cannot satisfy is built here from source so the compile is
+# cached as an image layer rather than repeated in every job.
+#
+# Debian does not package Google's crc32c library, so it is built here for the
+# google-crc32c C extension.
 FROM debian:sid
 
 RUN apt-get update -qq && apt-get install -y -qq --no-install-recommends \
-        build-essential cmake git python3 python3-dev python3-pip python3-venv \
+        build-essential cmake cython3 git meson ninja-build pkgconf python3 python3-dev \
+        python3-mesonpy python3-pip python3-setuptools-scm python3-venv \
         python3-crc32c python3-donfig python3-fsspec python3-hatch-vcs python3-hatchling \
         python3-hypothesis python3-numcodecs python3-numpy python3-numpydoc python3-packaging \
         python3-pytest python3-pytest-asyncio python3-pytest-benchmark python3-pytest-xdist \
@@ -24,3 +33,9 @@ RUN git clone -q --depth 1 --branch 1.1.2 https://github.com/google/crc32c /tmp/
 RUN python3 -m venv --system-site-packages /venv
 ENV PATH=/venv/bin:$PATH
 RUN pip install -q --no-binary google-crc32c google-crc32c msgspec pytest-accept
+# Debian sid ships numcodecs 0.17.0, which zarr excludes (see pyproject.toml; GHSA-jqc8-qjfv-5m6r),
+# and PyPI has no s390x wheels, so build a satisfying numcodecs from source into the venv, where
+# it shadows the Debian package. Built without isolation so the Debian meson, Cython and numpy
+# are used instead of compiling a build-time numpy under emulation. Remove once Debian ships a
+# version that satisfies zarr's constraint; `pip check` in the workflow will say when it does not.
+RUN pip install -q --no-binary numcodecs --no-build-isolation "numcodecs>=0.16.6,!=0.17.0"