diff --git a/.github/workflows/check-colab-notebooks.yml b/.github/workflows/check-colab-notebooks.yml
index 70a6eaade..dbf28f8a8 100644
--- a/.github/workflows/check-colab-notebooks.yml
+++ b/.github/workflows/check-colab-notebooks.yml
@@ -21,6 +21,8 @@ jobs:
     steps:
       - name: Checkout code
         uses: actions/checkout@3d3c42e5aac5ba805825da76410c181273ba90b1 # v7.0.1
+        with:
+          fetch-depth: 0
 
       - name: Install uv
         uses: astral-sh/setup-uv@c771a70e6277c0a99b617c7a806ffedaca235ff9 # v9.0.0
@@ -32,19 +34,46 @@ jobs:
       - name: Install dependencies
         run: uv sync --all-packages --group notebooks --group docs
 
+      - name: Get changed notebook sources
+        id: changed
+        env:
+          BASE_SHA: ${{ github.event.pull_request.base.sha || github.event.before }}
+        run: |
+          if [ -z "$BASE_SHA" ] || [ "$BASE_SHA" = "0000000000000000000000000000000000000000" ]; then
+            echo "full=true" >> "$GITHUB_OUTPUT"
+            exit 0
+          fi
+
+          while IFS= read -r -d '' source_path; do
+            printf '%s\0' "${source_path##*/}"
+          done < <(git diff --no-renames --name-only -z --diff-filter=ACDMT "$BASE_SHA" "$GITHUB_SHA" -- 'docs/notebook_source/*.py') > "$RUNNER_TEMP/changed-notebook-sources"
+
+          while IFS= read -r -d '' source_path; do
+            printf '%s\0' "${source_path##*/}"
+          done < <(git diff --no-renames --name-only -z --diff-filter=D "$BASE_SHA" "$GITHUB_SHA" -- 'docs/notebook_source/*.py') > "$RUNNER_TEMP/deleted-notebook-sources"
+
       - name: Generate Colab notebooks
+        env:
+          FULL_REGENERATION: ${{ steps.changed.outputs.full }}
         run: |
-          make generate-colab-notebooks
+          if [ "$FULL_REGENERATION" = "true" ]; then
+            make generate-colab-notebooks
+            exit 0
+          fi
+
+          while IFS= read -r -d '' file; do
+            rm -f "docs/colab_notebooks/${file%.py}.ipynb"
+          done < "$RUNNER_TEMP/deleted-notebook-sources"
+
+          make generate-colab-notebooks FILES_FILE="$RUNNER_TEMP/changed-notebook-sources"
 
       - name: Check for differences
         run: |
-          # Get the diff, filtering out cell ID changes (which are randomly generated)
-          # Filter out: file markers (--- and +++), and "id" lines
+          # Jupytext assigns random cell IDs, so ignore ID-only changes.
+          git add -N docs/colab_notebooks/
           MEANINGFUL_DIFF=$(git diff docs/colab_notebooks/ | grep -E '^[+-]' | grep -v '^---' | grep -v '^+++' | grep -vE '^[+-]\s*"id": "[0-9a-fA-F]+",?$' || true)
 
-          if [ -z "$MEANINGFUL_DIFF" ]; then
-            echo "✅ Colab notebooks are up-to-date (ignoring cell ID changes)"
-          else
+          if [ -n "$MEANINGFUL_DIFF" ]; then
             echo "❌ Colab notebooks are out of sync with source files"
             echo ""
             echo "The generated notebooks differ from the committed ones."
diff --git a/Makefile b/Makefile
index 842d8452e..cf8075a08 100644
--- a/Makefile
+++ b/Makefile
@@ -584,7 +584,13 @@ endif
 
 generate-colab-notebooks:
 	@echo "📓 Generating Colab-compatible notebooks ($(DOCS_PYTHON))..."
+ifdef FILES_FILE
+	@if [ -s "$(FILES_FILE)" ]; then \
+		xargs -0 -n 1 $(DOCS_PYTHON) docs/scripts/generate_colab_notebooks.py --files < "$(FILES_FILE)"; \
+	fi
+else
 	$(DOCS_PYTHON) docs/scripts/generate_colab_notebooks.py
+endif
 	@echo "✅ Colab notebooks created in docs/colab_notebooks/"
 
 generate-fern-notebooks: