diff --git a/.github/workflows/spec_zero.yml b/.github/workflows/spec_zero.yml
index 81f9a76476f..8511a40b005 100644
--- a/.github/workflows/spec_zero.yml
+++ b/.github/workflows/spec_zero.yml
@@ -46,8 +46,12 @@ jobs:
           version: ">=0.9"
           activate-environment: true
           python-version: 3.12
-      - run: uv pip install packaging requests tomlkit
-      - run: python ./tools/dev/spec_zero_update_versions.py
+      - name: Install dependencies
+        run: uv pip install -e . packaging requests tomlkit
+      - name: Update tracked dependencies
+        run: python ./tools/dev/spec_zero_update_versions.py
+      - name: Sync updated dependencies to README
+        run: python tools/sync_dependencies.py
       - name: Create lockfile for old CI
         # uv pip compile requires setting the python version explicitly in the command :(
         run: |
@@ -72,7 +76,9 @@ jobs:
           git config --global user.email "50266005+mne-bot@users.noreply.github.com"
           git config --global user.name "mne[bot]"
           git checkout -b spec_zero
-          git add doc/changes/dev/dependency.rst  # one new file, others changed
+          if [ -f doc/changes/dev/dependency.rst ]; then
+            git add doc/changes/dev/dependency.rst  # one new file, others changed
+          fi
           git commit -am "mne[bot]: Update dependency specifiers"
           git push origin spec_zero
           PR_NUM=$(gh pr create --base main --head spec_zero --title "MAINT: Update dependency specifiers" --body "Created by spec_zero [GitHub action](https://github.com/mne-tools/mne-python/actions/runs/${{ github.run_id }}). <br> <br> *Adjustments may need to be made to shims in \`mne/fixes.py\` and elswhere in this or another PR. \`make -C tools/dev dep\` is a good starting point for finding potential updates.*")
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 7007bf02255..465c009fcf9 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -71,14 +71,6 @@ repos:
         language: python
         entry: ./tools/hooks/update_environment_file.py
         files: '^(pyproject.toml|tools/hooks/update_environment_file.py)$'
-  - repo: local
-    hooks:
-      - id: dependency-sync
-        name: Copy core dependencies from pyproject.toml to README.rst
-        language: python
-        entry: ./tools/hooks/sync_dependencies.py
-        files: '^(pyproject.toml|tools/hooks/sync_dependencies.py)$'
-        additional_dependencies: ["mne==1.12.0"]
 
   # zizmor
   - repo: https://github.com/woodruffw/zizmor-pre-commit
@@ -89,10 +81,6 @@ repos:
         # We correctly use pull_request_trigger, and need Zizmor 2.0+ to configure the ignore
         exclude: ^.github/workflows/automerge.yml
 
-# these should *not* be run on CIs:
-ci:
-  skip: [dependency-sync]  # needs MNE to work, which exceeds the free tier space alloc.
-
 # The following are too slow to run on local commits, so let's only run on CIs:
 #
 #   - repo: https://github.com/pre-commit/mirrors-mypy
diff --git a/tools/environment_old.yml b/tools/environment_old.yml
deleted file mode 100644
index 6a9430496cb..00000000000
--- a/tools/environment_old.yml
+++ /dev/null
@@ -1,18 +0,0 @@
-# THIS FILE IS AUTO-GENERATED BY tools/hooks/update_environment_file.py AND WILL BE OVERWRITTEN
-name: mne
-channels:
-  - conda-forge
-dependencies:
-  - python =3.10
-  - numpy =1.26
-  - scipy =1.12
-  - matplotlib =3.8
-  - pandas =2.2
-  - scikit-learn =1.4
-  - nibabel
-  - tqdm
-  - pooch =1.5
-  - decorator
-  - packaging
-  - jinja2
-  - lazy_loader =0.3
diff --git a/tools/hooks/sync_dependencies.py b/tools/sync_dependencies.py
similarity index 98%
rename from tools/hooks/sync_dependencies.py
rename to tools/sync_dependencies.py
index 1ff6d7f8712..53f6dfc33f2 100755
--- a/tools/hooks/sync_dependencies.py
+++ b/tools/sync_dependencies.py
@@ -15,7 +15,7 @@
 
 from mne.utils import _pl, warn
 
-README_PATH = Path(__file__).parents[2] / "README.rst"
+README_PATH = Path(__file__).parents[1] / "README.rst"
 BEGIN = ".. ↓↓↓ BEGIN CORE DEPS LIST. DO NOT EDIT! HANDLED BY PRE-COMMIT HOOK ↓↓↓"
 END = ".. ↑↑↑ END CORE DEPS LIST. DO NOT EDIT! HANDLED BY PRE-COMMIT HOOK ↑↑↑"
 
