diff --git a/.github/workflows/upstream-dev-ci.yaml b/.github/workflows/upstream-dev-ci.yaml
index 411c3e3a73e..7936743277b 100644
--- a/.github/workflows/upstream-dev-ci.yaml
+++ b/.github/workflows/upstream-dev-ci.yaml
@@ -58,6 +58,10 @@ jobs:
         )
       )
 
+    env:
+      MANIFEST_PATH: ci/nightly/pixi.toml
+      LOCK_PATH: ci/nightly/pixi.lock
+
     outputs:
       cache-key: ${{ steps.pixi-lock.outputs.cache-key }}
       pixi-version: ${{ steps.pixi-lock.outputs.pixi-version }}
@@ -65,12 +69,17 @@ jobs:
       - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
         with:
           persist-credentials: false
-      - uses: Parcels-code/pixi-lock/create-and-cache@38495788b79a5ff26009aecc15daa9a8310b8832 # v0.1.0
+      - uses: Parcels-code/pixi-lock/create-and-cache@1fab4c17af8243f6ca1321bc941cf2325f46c05d # v0.1.1
         id: pixi-lock
+        with:
+          manifest-path: ${{ env.MANIFEST_PATH }}
+          hash-files: |
+            ${{ env.MANIFEST_PATH }}
+            pyproject.toml
       - uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7.0.1
         with:
           name: pixi-lock
-          path: pixi.lock
+          path: ${{ env.LOCK_PATH }}
 
   upstream-dev:
     name: upstream-dev
@@ -89,6 +98,7 @@ jobs:
 
     env:
       ENV: ${{ matrix.pixi-env }}
+      MANIFEST_PATH: ci/nightly/pixi.toml
 
     outputs:
       log-file: ${{ steps.determine-log-path.outputs.log-file }}
@@ -102,31 +112,35 @@ jobs:
         id: determine-log-path
         run: |
           echo "log-file=output-${ENV}-log.jsonl" >> $GITHUB_OUTPUT;
-          cat $GITHUB_OUTPUT
       - name: Restore cached pixi lockfile
-        uses: Parcels-code/pixi-lock/restore@38495788b79a5ff26009aecc15daa9a8310b8832 # v0.1.0
+        uses: Parcels-code/pixi-lock/restore@1fab4c17af8243f6ca1321bc941cf2325f46c05d # v0.1.1
         with:
+          manifest-path: ${{ env.MANIFEST_PATH }}
           cache-key: ${{ needs.cache-pixi-lock.outputs.cache-key }}
       - uses: prefix-dev/setup-pixi@a09b6247153796b190642a2b53fac4241043cf6f # v0.10.0
         with:
           pixi-version: ${{ needs.cache-pixi-lock.outputs.pixi-version }}
           cache: true
           environments: ${{ matrix.pixi-env }}
+          manifest-path: ${{ env.MANIFEST_PATH }}
           cache-write: ${{ github.event_name == 'push' && github.ref_name == 'main' }}
       - name: Version info
         run: |
-          pixi run -e $ENV -- python xarray/util/print_versions.py
+          pixi run --manifest-path "$MANIFEST_PATH" -e $ENV -- python xarray/util/print_versions.py
       - name: Import xarray
         run: |
-          pixi run -e $ENV -- python -c 'import xarray'
+          pixi run --manifest-path "$MANIFEST_PATH" -e $ENV -- python -c 'import xarray'
       - name: Run Tests
         if: success()
         id: status
         env:
           LOG_PATH: ${{ steps.determine-log-path.outputs.log-file }}
         run: |
-          pixi run -e $ENV -- python -m pytest --timeout=60 -rf -nauto \
-            --report-log "$LOG_PATH"
+          pixi run \
+            --manifest-path "$MANIFEST_PATH" \
+            -e $ENV \
+            -- \
+            python -m pytest --timeout=60 -rf -nauto --report-log "$LOG_PATH"
       - uses: actions/upload-artifact@043fb46d1a93c77aae656e7c1c64a875d1fc6a0a # v7.0.1
         if: failure()
         with:
@@ -174,6 +188,7 @@ jobs:
 
     env:
       ENV: ${{ matrix.pixi-env }}
+      MANIFEST_PATH: ci/nightly/pixi.toml
 
     steps:
       - uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
@@ -182,26 +197,28 @@ jobs:
           persist-credentials: false
 
       - name: Restore cached pixi lockfile
-        uses: Parcels-code/pixi-lock/restore@38495788b79a5ff26009aecc15daa9a8310b8832 # v0.1.0
+        uses: Parcels-code/pixi-lock/restore@1fab4c17af8243f6ca1321bc941cf2325f46c05d # v0.1.1
         with:
+          manifest-path: ${{ env.MANIFEST_PATH }}
           cache-key: ${{ needs.cache-pixi-lock.outputs.cache-key }}
       - uses: prefix-dev/setup-pixi@a09b6247153796b190642a2b53fac4241043cf6f # v0.10.0
         with:
           pixi-version: ${{ needs.cache-pixi-lock.outputs.pixi-version }}
           cache: true
           environments: ${{ matrix.pixi-env }}
+          manifest-path: ${{ env.MANIFEST_PATH }}
           cache-write: ${{ github.event_name == 'push' && github.ref_name == 'main' }}
 
       - name: set environment variables
         run: |
           echo "TODAY=$(date +'%Y-%m-%d')" >> $GITHUB_ENV
-          echo "PYTHON_VERSION=$(pixi run -e $ENV -- python --version | cut -d' ' -f2 | cut -d. -f1,2)" >> $GITHUB_ENV
+          echo "PYTHON_VERSION=$(pixi run --manifest-path "$MANIFEST_PATH" -e $ENV -- python --version | cut -d' ' -f2 | cut -d. -f1,2)" >> $GITHUB_ENV
       - name: Version info
         run: |
-          pixi run -e $ENV -- python xarray/util/print_versions.py
+          pixi run --manifest-path "$MANIFEST_PATH" -e $ENV -- python xarray/util/print_versions.py
       - name: Run mypy
         run: |
-          pixi run -e $ENV -- python -m mypy --install-types --non-interactive --cobertura-xml-report mypy_report
+          pixi run --manifest-path "$MANIFEST_PATH" -e $ENV -- python -m mypy --install-types --non-interactive --cobertura-xml-report mypy_report
       - name: Upload mypy coverage to Codecov
         uses: codecov/codecov-action@fb8b3582c8e4def4969c97caa2f19720cb33a72f # v7.0.0
         with:
diff --git a/.readthedocs.yaml b/.readthedocs.yaml
index f2ea760edc9..fa081448061 100644
--- a/.readthedocs.yaml
+++ b/.readthedocs.yaml
@@ -14,6 +14,7 @@ build:
       - asdf plugin add pixi
       - asdf install pixi latest
       - asdf global pixi latest
+      - pixi lock --no-install
     post_checkout:
       - (git --no-pager log --pretty="tformat:%s" -1 | grep -vqF "[skip-rtd]") || exit 183
       - git fetch --unshallow || true
diff --git a/ci/nightly/pixi.toml b/ci/nightly/pixi.toml
new file mode 100644
index 00000000000..0f4f640c95e
--- /dev/null
+++ b/ci/nightly/pixi.toml
@@ -0,0 +1,146 @@
+[workspace]
+preview = ["pixi-build"]
+channels = ["conda-forge", "nodefaults"]
+platforms = ["linux-64"]
+requires-pixi = ">=0.63.2,!=0.68.0"
+
+[feature.test.dependencies]
+pytest = "!=9.1.0"
+pytest-asyncio = "*"
+pytest-cov = "*"
+pytest-env = "*"
+pytest-mypy-plugins = ">=4.0.0"
+pytest-reportlog = "*"
+pytest-timeout = "*"
+pytest-xdist = "*"
+pytz = "*"
+hypothesis = "*"
+coveralls = "*"
+
+[feature.test.tasks]
+test = { cmd = "pytest", description = "Run the test suite with pytest." }
+
+[feature.py314.dependencies]
+python = "3.14.*"
+
+# TODO: Remove `target.unix` restriction once pandas nightly has win-64 wheels again.
+# Without this, `pixi lock` fails because it can't solve the nightly feature for win-64,
+# which breaks RTD builds (RTD has no lock file cache, unlike GitHub Actions CI).
+[feature.nightly.target.unix.dependencies]
+python = "*"
+
+[feature.nightly.pypi-options.dependency-overrides]
+numpy = { version = "*", index = "https://pypi.anaconda.org/scientific-python-nightly-wheels/simple" }
+scipy = { version = "*", index = "https://pypi.anaconda.org/scientific-python-nightly-wheels/simple" }
+matplotlib = { version = "*", index = "https://pypi.anaconda.org/scientific-python-nightly-wheels/simple" }
+pandas = { version = "*", index = "https://pypi.anaconda.org/scientific-python-nightly-wheels/simple" }
+pyarrow = { version = "*", index = "https://pypi.anaconda.org/scientific-python-nightly-wheels/simple" }
+
+dask = { git = "https://github.com/dask/dask" }
+distributed = { git = "https://github.com/dask/distributed" }
+zarr = { git = "https://github.com/zarr-developers/zarr-python" }
+# numcodecs = { git = "https://github.com/zarr-developers/numcodecs" }  #? compilation fails currently, see #11437
+cftime = { git = "https://github.com/Unidata/cftime" }
+# packaging = { git = "https://github.com/pypa/packaging"} #? Pixi warns if this is enabled
+pint = { git = "https://github.com/hgrecco/pint" }
+bottleneck = { git = "https://github.com/pydata/bottleneck" }
+fsspec = { git = "https://github.com/intake/filesystem_spec" }
+nc-time-axis = { git = "https://github.com/SciTools/nc-time-axis" }
+flox = { git = "https://github.com/xarray-contrib/flox" }
+h5netcdf = { git = "https://github.com/h5netcdf/h5netcdf" }
+opt_einsum = { git = "https://github.com/dgasmith/opt_einsum" }
+# sparse = { git = "https://github.com/pydata/sparse"}
+
+[feature.nightly.target.unix.pypi-dependencies]
+xarray = { path = "../..", editable = true }
+numpy = "*"
+pandas = "*"
+matplotlib = "*"
+scipy = "*"
+pyarrow = "*"
+
+dask = "*"
+distributed = "*"
+zarr = "*"
+numcodecs = "*"
+cftime = "*"
+packaging = "*"
+pint = "*"
+bottleneck = "*"
+fsspec = "*"
+nc-time-axis = "*"
+flox = "*"
+# h5netcdf = "*"
+# h5py = "*"
+opt_einsum = "*"
+netcdf4 = "*"
+scitools-iris = "*"
+pydap = "*"
+cartopy = "*"
+seaborn = "*"
+
+[feature.typing.dependencies]
+mypy = "==1.19.1"
+pyright = "*"
+hypothesis = "*"
+lxml = "*"
+types-colorama = "*"
+types-docutils = "*"
+types-decorator = "*"
+types-networkx = "*"
+types-openpyxl = "*"
+types-psutil = "*"
+types-Pygments = "*"
+types-python-dateutil = "*"
+types-pytz = "*"
+types-PyYAML = "*"
+types-requests = "*"
+types-setuptools = "*"
+typing_extensions = "*"
+pip = "*"
+
+[feature.typing.pypi-dependencies]
+types-defusedxml = "*"
+types-pexpect = "*"
+
+# Stubs sourced from PyPI rather than conda, used only by the `mypy-upstream`
+# environment. That env pairs the `nightly` feature (which overrides numpy/scipy
+# to PyPI nightly wheels) with type stubs; conda stubs would pull conda
+# numpy/scipy that pixi cannot reconcile with those PyPI overrides, so they must
+# come from PyPI here.
+#
+# NOTE: these stubs cap numpy below the nightly wheel (scipy-stubs via optype ->
+# numpy-typing-compat needs numpy<2.5; pandas-stubs needs numpy<=2.3.5), so numpy
+# in `mypy-upstream` resolves to the latest release. We accept that: dropping the
+# stubs to free up numpy would leave pandas/scipy untyped and flood mypy with
+# import-untyped errors. The upstream *test* job (`test-nightly`) is kept separate
+# precisely so it still gets the genuine nightly numpy.
+[feature.typing-stubs-nightly.pypi-dependencies]
+pandas-stubs = "<=2.3.3.251219"
+scipy-stubs = ">=1.17.1.2"
+
+[feature.typing.tasks]
+mypy = { cmd = "mypy --install-types --non-interactive --cobertura-xml-report mypy_report", description = "Run mypy type checking and generate a Cobertura XML report." }
+
+[environments]
+test-nightly = { features = [
+  "py314",
+  "nightly",
+  "test",
+  # Deliberately no "typing": type stubs cap numpy<2.5 and would displace the
+  # nightly numpy wheel this env's pytest job needs. Type checking against the
+  # dev stack lives in the separate `mypy-upstream` environment below.
+], no-default-feature = true }
+
+# Type-checking against the development stack (used by the `mypy-upstream-dev` CI
+# job). Same as `test-nightly` plus the typing toolchain and PyPI-sourced stubs.
+# numpy resolves to the latest release here (the stubs cap it below the nightly
+# wheel); every other dependency still comes from the nightly wheels / git, so
+# this catches typing breakage from upstream development versions.
+mypy-upstream = { features = [
+  "py314",
+  "nightly",
+  "test",
+  "typing",
+  "typing-stubs-nightly",
+], no-default-feature = true }
diff --git a/pixi.toml b/pixi.toml
index 0ae5b4341c2..52dda513e46 100644
--- a/pixi.toml
+++ b/pixi.toml
@@ -143,62 +143,6 @@ toolz = "1.0.*"
 zarr = "3.0.*"
 pyarrow = "*"        # required by dask.dataframe
 
-# TODO: Remove `target.unix` restriction once pandas nightly has win-64 wheels again.
-# Without this, `pixi lock` fails because it can't solve the nightly feature for win-64,
-# which breaks RTD builds (RTD has no lock file cache, unlike GitHub Actions CI).
-[feature.nightly.target.unix.dependencies]
-python = "*"
-
-[feature.nightly.pypi-options.dependency-overrides]
-numpy = { version = "*", index = "https://pypi.anaconda.org/scientific-python-nightly-wheels/simple" }
-scipy = { version = "*", index = "https://pypi.anaconda.org/scientific-python-nightly-wheels/simple" }
-matplotlib = { version = "*", index = "https://pypi.anaconda.org/scientific-python-nightly-wheels/simple" }
-pandas = { version = "*", index = "https://pypi.anaconda.org/scientific-python-nightly-wheels/simple" }
-pyarrow = { version = "*", index = "https://pypi.anaconda.org/scientific-python-nightly-wheels/simple" }
-
-dask = { git = "https://github.com/dask/dask" }
-distributed = { git = "https://github.com/dask/distributed" }
-zarr = { git = "https://github.com/zarr-developers/zarr-python" }
-# numcodecs = { git = "https://github.com/zarr-developers/numcodecs" }  #? compilation fails currently, see #11437
-cftime = { git = "https://github.com/Unidata/cftime" }
-# packaging = { git = "https://github.com/pypa/packaging"} #? Pixi warns if this is enabled
-pint = { git = "https://github.com/hgrecco/pint" }
-bottleneck = { git = "https://github.com/pydata/bottleneck" }
-fsspec = { git = "https://github.com/intake/filesystem_spec" }
-nc-time-axis = { git = "https://github.com/SciTools/nc-time-axis" }
-flox = { git = "https://github.com/xarray-contrib/flox" }
-h5netcdf = { git = "https://github.com/h5netcdf/h5netcdf" }
-opt_einsum = { git = "https://github.com/dgasmith/opt_einsum" }
-# sparse = { git = "https://github.com/pydata/sparse"}
-
-[feature.nightly.target.unix.pypi-dependencies]
-xarray = { path = ".", editable = true }
-
-numpy = "*"
-pandas = "*"
-matplotlib = "*"
-scipy = "*"
-pyarrow = "*"
-
-dask = "*"
-distributed = "*"
-zarr = "*"
-numcodecs = "*"
-cftime = "*"
-packaging = "*"
-pint = "*"
-bottleneck = "*"
-fsspec = "*"
-nc-time-axis = "*"
-flox = "*"
-# h5netcdf = "*"
-# h5py = "*"
-opt_einsum = "*"
-netcdf4 = "*"
-scitools-iris = "*"
-pydap = "*"
-cartopy = "*"
-seaborn = "*"
 
 [feature.test.dependencies]
 pytest = "!=9.1.0"
@@ -300,22 +244,6 @@ types-pexpect = "*"
 pandas-stubs = "<=2.3.3.251219"
 scipy-stubs = ">=1.17.1.2"
 
-# Stubs sourced from PyPI rather than conda, used only by the `mypy-upstream`
-# environment. That env pairs the `nightly` feature (which overrides numpy/scipy
-# to PyPI nightly wheels) with type stubs; conda stubs would pull conda
-# numpy/scipy that pixi cannot reconcile with those PyPI overrides, so they must
-# come from PyPI here.
-#
-# NOTE: these stubs cap numpy below the nightly wheel (scipy-stubs via optype ->
-# numpy-typing-compat needs numpy<2.5; pandas-stubs needs numpy<=2.3.5), so numpy
-# in `mypy-upstream` resolves to the latest release. We accept that: dropping the
-# stubs to free up numpy would leave pandas/scipy untyped and flood mypy with
-# import-untyped errors. The upstream *test* job (`test-nightly`) is kept separate
-# precisely so it still gets the genuine nightly numpy.
-[feature.typing-stubs-nightly.pypi-dependencies]
-pandas-stubs = "<=2.3.3.251219"
-scipy-stubs = ">=1.17.1.2"
-
 [feature.typing.tasks]
 mypy = { cmd = "mypy --install-types --non-interactive --cobertura-xml-report mypy_report", description = "Run mypy type checking and generate a Cobertura XML report." }
 
@@ -393,6 +321,9 @@ numpydoc-lint = { cmd = "python ci/numpydoc-public-api.py" }
 [feature.nodask.constraints]
 dask-core = "<0.0a0"
 
+[feature.nightly.dependencies]
+python = "*"
+
 [environments]
 # Testing
 # test-just-xarray = { features = ["test"] } # https://github.com/pydata/xarray/pull/10888/files#r2511336147
@@ -435,28 +366,6 @@ test-py314 = { features = [
   "viz",
   "extras",
 ] }
-test-nightly = { features = [
-  "py313",
-  "nightly",
-  "test",
-  # Deliberately no "typing": type stubs cap numpy<2.5 and would displace the
-  # nightly numpy wheel this env's pytest job needs. Type checking against the
-  # dev stack lives in the separate `mypy-upstream` environment below.
-], no-default-feature = true }
-
-# Type-checking against the development stack (used by the `mypy-upstream-dev` CI
-# job). Same as `test-nightly` plus the typing toolchain and PyPI-sourced stubs.
-# numpy resolves to the latest release here (the stubs cap it below the nightly
-# wheel); every other dependency still comes from the nightly wheels / git, so
-# this catches typing breakage from upstream development versions.
-mypy-upstream = { features = [
-  "py313",
-  "nightly",
-  "test",
-  "typing",
-  "typing-stubs-nightly",
-], no-default-feature = true }
-
 
 test-py311 = { features = [
   "py311",
@@ -535,3 +444,4 @@ default = { features = [
 policy = { features = ["policy"], no-default-feature = true }
 numpydoc-lint = { features = ["numpydoc-lint"] }
 tools = { features = ["tools"], no-default-feature = true }
+test-nightly = { features = ["nightly"], no-default-feature = true }