diff --git a/.github/workflows/__autobuild-direct-tracing-with-working-dir.yml b/.github/workflows/__autobuild-direct-tracing-with-working-dir.yml
new file mode 100644
index 0000000000..5d2ba7c2de
--- /dev/null
+++ b/.github/workflows/__autobuild-direct-tracing-with-working-dir.yml
@@ -0,0 +1,92 @@
+# Warning: This file is generated automatically, and should not be modified.
+# Instead, please modify the template in the pr-checks directory and run:
+#     (cd pr-checks; pip install ruamel.yaml@0.17.31 && python3 sync.py)
+# to regenerate this file.
+
+name: PR Check - Autobuild direct tracing (custom working directory)
+env:
+  GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
+  GO111MODULE: auto
+  CODEQL_EXTRACTOR_JAVA_AGENT_DISABLE_KOTLIN: 'true'
+on:
+  push:
+    branches:
+      - main
+      - releases/v*
+  pull_request:
+    types:
+      - opened
+      - synchronize
+      - reopened
+      - ready_for_review
+  schedule:
+    - cron: '0 5 * * *'
+  workflow_dispatch: {}
+jobs:
+  autobuild-direct-tracing-with-working-dir:
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - os: ubuntu-latest
+            version: linked
+          - os: windows-latest
+            version: linked
+          - os: ubuntu-latest
+            version: nightly-latest
+          - os: windows-latest
+            version: nightly-latest
+    name: Autobuild direct tracing (custom working directory)
+    permissions:
+      contents: read
+      security-events: write
+    timeout-minutes: 45
+    runs-on: ${{ matrix.os }}
+    steps:
+      - name: Setup Python on MacOS
+        uses: actions/setup-python@v5
+        if: >-
+          runner.os == 'macOS' && (
+
+          matrix.version == 'stable-20230403' ||
+
+          matrix.version == 'stable-v2.13.5' ||
+
+          matrix.version == 'stable-v2.14.6')
+        with:
+          python-version: '3.11'
+      - name: Check out repository
+        uses: actions/checkout@v4
+      - name: Prepare test
+        id: prepare-test
+        uses: ./.github/actions/prepare-test
+        with:
+          version: ${{ matrix.version }}
+          use-all-platform-bundle: 'false'
+      - name: Test setup
+        shell: bash
+        run: |
+          # Make sure that Gradle build succeeds in autobuild-dir ...
+          cp -a ../action/tests/java-repo autobuild-dir
+          # ... and fails if attempted in the current directory
+          echo > build.gradle
+      - uses: ./../action/init
+        with:
+          build-mode: autobuild
+          languages: java
+          tools: ${{ steps.prepare-test.outputs.tools-url }}
+      - name: Check that indirect tracing is disabled
+        shell: bash
+        run: |
+          if [[ ! -z "${CODEQL_RUNNER}" ]]; then
+            echo "Expected indirect tracing to be disabled, but the" \
+              "CODEQL_RUNNER environment variable is set."
+            exit 1
+          fi
+      - uses: ./../action/autobuild
+        with:
+          working-directory: autobuild-dir
+      - uses: ./../action/analyze
+    env:
+      CODEQL_ACTION_AUTOBUILD_BUILD_MODE_DIRECT_TRACING: true
+      CODEQL_ACTION_TEST_MODE: true
diff --git a/pr-checks/checks/autobuild-direct-tracing-with-working-dir.yml b/pr-checks/checks/autobuild-direct-tracing-with-working-dir.yml
new file mode 100644
index 0000000000..e6ba989176
--- /dev/null
+++ b/pr-checks/checks/autobuild-direct-tracing-with-working-dir.yml
@@ -0,0 +1,34 @@
+name: "Autobuild direct tracing (custom working directory)"
+description: >
+  An end-to-end integration test of a Java repository built using 'build-mode: autobuild',
+  with direct tracing enabled and a custom working directory specified as the input to the
+  autobuild Action.
+operatingSystems: ["ubuntu", "windows"]
+versions: ["linked", "nightly-latest"]
+env:
+  CODEQL_ACTION_AUTOBUILD_BUILD_MODE_DIRECT_TRACING: true
+steps:
+  - name: Test setup
+    shell: bash
+    run: |
+      # Make sure that Gradle build succeeds in autobuild-dir ...
+      cp -a ../action/tests/java-repo autobuild-dir
+      # ... and fails if attempted in the current directory
+      echo > build.gradle
+  - uses: ./../action/init
+    with:
+      build-mode: autobuild
+      languages: java
+      tools: ${{ steps.prepare-test.outputs.tools-url }}
+  - name: Check that indirect tracing is disabled
+    shell: bash
+    run: |
+      if [[ ! -z "${CODEQL_RUNNER}" ]]; then
+        echo "Expected indirect tracing to be disabled, but the" \
+          "CODEQL_RUNNER environment variable is set."
+        exit 1
+      fi
+  - uses: ./../action/autobuild
+    with:
+      working-directory: autobuild-dir
+  - uses: ./../action/analyze