diff --git a/.github/workflows/notebook-test.yml b/.github/workflows/notebook-test.yml
index e81ac4cae61..839f97e62f2 100644
--- a/.github/workflows/notebook-test.yml
+++ b/.github/workflows/notebook-test.yml
@@ -25,39 +25,42 @@ jobs:
     steps:
       - uses: actions/checkout@v4
 
-      - name: Get all changed notebooks
-        id: all-changed-notebooks
+      - name: Get relevant changed files
+        id: all-changed
         uses: tj-actions/changed-files@af2816c65436325c50621100d67f6e853cd1b0f1
         with:
-          files: "docs/**/*.ipynb"
+          files: "{docs/**/*.ipynb,scripts/nb-tester/**/*}"
           separator: "\n"
           write_output_files: true
 
-      - name: Get changed config files
-        id: changed-config
-        uses: tj-actions/changed-files@af2816c65436325c50621100d67f6e853cd1b0f1
-        with:
-          files: "scripts/nb-tester/**/*"
-          write_output_files: true
-
-      - name: Check for notebooks that require Linux
-        id: linux-changed-files
-        uses: tj-actions/changed-files@af2816c65436325c50621100d67f6e853cd1b0f1
-        with:
+      - name: Check if extra linux deps needed
+        id: check-deps
+        shell: python
+        run: |
           # Add your notebook to this list if it needs latex or graphviz to run
-          files: |
-            docs/guides/visualize-circuits.ipynb
-            docs/guides/custom-backend.ipynb
-            docs/guides/transpiler-stages.ipynb
-            docs/guides/represent-quantum-computers.ipynb
-            docs/guides/common-parameters.ipynb
+          EXTRA_DEPS_NOTEBOOKS = """\
+          docs/guides/visualize-circuits.ipynb
+          docs/guides/custom-backend.ipynb
+          docs/guides/transpiler-stages.ipynb
+          docs/guides/represent-quantum-computers.ipynb
+          docs/guides/common-parameters.ipynb
+          """.strip().split("\n")
+          import os
+          github_output = os.getenv("GITHUB_OUTPUT")
+          all_files = "${{ steps.all-changed.outputs.all_changed_files }}".split("\n")
+
+          config_changed = any(path.startswith("scripts/") for path in all_files)
+          extra_deps = config_changed or any(path in EXTRA_DEPS_NOTEBOOKS for path in all_files)
+
+          with open(github_output, "a") as output:
+            output.write(f"NEEDS_EXTRA_DEPS={str(extra_deps).lower()}")
 
       - name: Setup environment
         uses: ./.github/actions/set-up-notebook-testing
         with:
           # Install Linux deps if the specific guides were changed, or
           # if all files are being tested.
-          install-linux-deps: ${{ steps.linux-changed-files.outputs.any_changed == 'true' || steps.changed-config.outputs.any_changed == 'true' }}
+          install-linux-deps: ${{ steps.check-deps.outputs.NEEDS_EXTRA_DEPS }}
           ibm-quantum-token: ${{ secrets.IBM_QUANTUM_TEST_TOKEN }}
 
       - name: Execute notebooks
diff --git a/scripts/ci/pr-execute-notebooks.py b/scripts/ci/pr-execute-notebooks.py
index ebc0851b377..d87404e87d6 100644
--- a/scripts/ci/pr-execute-notebooks.py
+++ b/scripts/ci/pr-execute-notebooks.py
@@ -32,16 +32,16 @@
 import subprocess
 from pathlib import Path
 
-changed_notebooks = Path(".github/outputs/all_changed_files.txt").read_text().split("\n")
-print(changed_notebooks)
-changed_config = Path(".github/outputs/changed-config.txt").read_text().split("\n")
+all_changed_files = Path(".github/outputs/all_changed_files.txt").read_text().split("\n")
 
-print(changed_notebooks)
-print()
-print(changed_config)
+changed_notebooks = [
+    path for path in all_changed_files
+    if path.startswith("docs/")
+]
+config_changed = any(path.startswith("scripts/") for path in all_changed_files)
 
 args = ["tox", "--", "--write"]
-if changed_notebooks and not changed_config:
+if changed_notebooks and not config_changed:
   args.extend(changed_notebooks.split("\n"))
 
 is_fork = os.environ["PR_REPOSITORY"] != os.environ["GITHUB_REPOSITORY"]