diff --git a/.github/workflows/__with-checkout-path.yml b/.github/workflows/__with-checkout-path.yml
index e15459fddd..f90bb198d5 100644
--- a/.github/workflows/__with-checkout-path.yml
+++ b/.github/workflows/__with-checkout-path.yml
@@ -96,27 +96,39 @@ jobs:
         )
       shell: bash
       run: echo "CODEQL_ENABLE_EXPERIMENTAL_FEATURES_SWIFT=true" >> $GITHUB_ENV
+    - name: Delete original checkout
+      shell: bash
+      run: |
+        rm -rf ./* .github
+  # Check out the actions repo again, but at a different location.
+  # choose an arbitrary SHA so that we can later test that the commit_oid is not from main
     - uses: actions/checkout@v4
       with:
         ref: 474bbf07f9247ffe1856c6a0f94aeeb10e7afee6
         path: x/y/z/some-path
+
     - uses: ./../action/init
       with:
         tools: ${{ steps.prepare-test.outputs.tools-url }}
       # it's enough to test one compiled language and one interpreted language
         languages: csharp,javascript
-        source-path: x/y/z/some-path/tests/multi-language-repo
+        source-root: x/y/z/some-path/tests/multi-language-repo
         debug: true
+
     - name: Build code (non-windows)
       shell: bash
       if: ${{ runner.os != 'Windows' }}
+      working-directory: x/y/z/some-path/tests/multi-language-repo
       run: |
-        $CODEQL_RUNNER x/y/z/some-path/tests/multi-language-repo/build.sh
+        $CODEQL_RUNNER build.sh
+
     - name: Build code (windows)
       shell: bash
       if: ${{ runner.os == 'Windows' }}
+      working-directory: x/y/z/some-path/tests/multi-language-repo
       run: |
-        x/y/z/some-path/tests/multi-language-repo/build.sh
+        build.sh
+
     - uses: ./../action/analyze
       with:
         checkout_path: x/y/z/some-path/tests/multi-language-repo
diff --git a/pr-checks/checks/with-checkout-path.yml b/pr-checks/checks/with-checkout-path.yml
index 42564c64ea..faa81b6396 100644
--- a/pr-checks/checks/with-checkout-path.yml
+++ b/pr-checks/checks/with-checkout-path.yml
@@ -1,29 +1,40 @@
 name: "Use a custom `checkout_path`"
 description: "Checks that a custom `checkout_path` will find the proper commit_oid"
 steps:
+  # This ensures we don't accidentally use the original checkout for any part of the test.
+  - name: Delete original checkout
+    shell: bash
+    run: |
+      rm -rf ./* .github
   # Check out the actions repo again, but at a different location.
   # choose an arbitrary SHA so that we can later test that the commit_oid is not from main
   - uses: actions/checkout@v4
     with:
       ref: 474bbf07f9247ffe1856c6a0f94aeeb10e7afee6
       path: x/y/z/some-path
+
   - uses: ./../action/init
     with:
       tools: ${{ steps.prepare-test.outputs.tools-url }}
       # it's enough to test one compiled language and one interpreted language
       languages: csharp,javascript
-      source-path: x/y/z/some-path/tests/multi-language-repo
+      source-root: x/y/z/some-path/tests/multi-language-repo
       debug: true
+
   - name: Build code (non-windows)
     shell: bash
     if: ${{ runner.os != 'Windows' }}
+    working-directory: x/y/z/some-path/tests/multi-language-repo
     run: |
-      $CODEQL_RUNNER x/y/z/some-path/tests/multi-language-repo/build.sh
+      $CODEQL_RUNNER build.sh
+
   - name: Build code (windows)
     shell: bash
     if: ${{ runner.os == 'Windows' }}
+    working-directory: x/y/z/some-path/tests/multi-language-repo
     run: |
-      x/y/z/some-path/tests/multi-language-repo/build.sh
+      build.sh
+
   - uses: ./../action/analyze
     with:
       checkout_path: x/y/z/some-path/tests/multi-language-repo