diff --git a/setup.cfg b/setup.cfg
index adf8c25d..42de93f1 100644
--- a/setup.cfg
+++ b/setup.cfg
@@ -35,3 +35,4 @@ filterwarnings =
     error
 markers=
     repo_suffix: Allows to use an additional suffix for the e2e test repo.
+    code_path: Allows to place the code in a subdirectory for the e2e test repo.
diff --git a/tests/end_to_end/conftest.py b/tests/end_to_end/conftest.py
index 50ee5087..ea8f9aaa 100644
--- a/tests/end_to_end/conftest.py
+++ b/tests/end_to_end/conftest.py
@@ -41,7 +41,7 @@ def _(command, *args, env, **kwargs):
 @contextlib.contextmanager
 def _cd(tmp_path: pathlib.Path, path: str):
     full_path = tmp_path / path
-    full_path.mkdir(exist_ok=True)
+    full_path.mkdir(exist_ok=True, parents=True)
     old_path = pathlib.Path.cwd()
     if old_path == full_path:
         yield full_path
@@ -191,18 +191,30 @@ def gh_other_username(gh_other):
 
 
 @pytest.fixture
-def git_repo(cd, git, action_ref):
+def git_repo(cd, git, action_ref, code_path):
     with cd("repo") as repo:
         git("init", "-b", "main")
+        # Copy .github
+        shutil.copytree(
+            pathlib.Path(__file__).parent / "repo" / ".github",
+            repo / ".github",
+            dirs_exist_ok=True,
+        )
+        # Copy everything else
         shutil.copytree(
             pathlib.Path(__file__).parent / "repo",
-            repo,
+            repo / code_path,
             dirs_exist_ok=True,
+            ignore=shutil.ignore_patterns(".github"),
         )
         # Rewrite the specific version of the action we run in the workflow files.
         for file in (repo / ".github/workflows").iterdir():
-            file: pathlib.Path
-            file.write_text(file.read_text().replace("__ACTION_REF__", action_ref))
+            content = (
+                file.read_text()
+                .replace("__ACTION_REF__", action_ref)
+                .replace("__ACTION_COVERAGE_PATH__", str(code_path))
+            )
+            file.write_text(content)
 
         git("add", ".")
         git("commit", "-m", "initial commit")
@@ -221,6 +233,12 @@ def repo_name(request):
     return name
 
 
+@pytest.fixture
+def code_path(request):
+    mark = request.node.get_closest_marker("code_path")
+    return pathlib.Path(*mark.args) if mark else pathlib.Path(".")
+
+
 @pytest.fixture
 def repo_full_name(repo_name, gh_me_username):
     return f"{gh_me_username}/{repo_name}"
@@ -378,9 +396,9 @@ def _(*, workflow_name, triggering_user, gh):
 
 
 @pytest.fixture
-def add_coverage_line(git):
+def add_coverage_line(git, code_path):
     def f(line):
-        csv_file = pathlib.Path("tests/cases.csv")
+        csv_file = pathlib.Path(code_path / "tests/cases.csv")
         csv_file.write_text(csv_file.read_text() + line + "\n")
 
         git("add", str(csv_file))
diff --git a/tests/end_to_end/repo/.github/workflows/ci.yml b/tests/end_to_end/repo/.github/workflows/ci.yml
index dbdc8bb8..18c7daf2 100644
--- a/tests/end_to_end/repo/.github/workflows/ci.yml
+++ b/tests/end_to_end/repo/.github/workflows/ci.yml
@@ -4,7 +4,7 @@ on:
   pull_request:
   push:
     branches:
-      - 'main'
+      - "main"
 
 concurrency:
   group: CI
@@ -17,7 +17,6 @@ jobs:
       pull-requests: write
       contents: write
     steps:
-
       - uses: actions/checkout@v3
 
       - name: Install poetry
@@ -25,12 +24,14 @@ jobs:
 
       - uses: actions/setup-python@v4
         with:
-          python-version: '3.10'
-          cache: 'poetry'
+          python-version: "3.10"
+          cache: "poetry"
 
       - run: poetry install
+        working-directory: __ACTION_COVERAGE_PATH__
 
       - run: poetry run pytest
+        working-directory: __ACTION_COVERAGE_PATH__
 
       - name: Coverage comment
         id: coverage_comment
@@ -39,6 +40,7 @@ jobs:
           GITHUB_TOKEN: ${{ github.token }}
           ANNOTATE_MISSING_LINES: true
           ANNOTATION_TYPE: notice
+          COVERAGE_PATH: __ACTION_COVERAGE_PATH__
 
       - name: Store Pull Request comment to be posted
         uses: actions/upload-artifact@v3
diff --git a/tests/end_to_end/repo/.github/workflows/coverage-comment.yml b/tests/end_to_end/repo/.github/workflows/coverage-comment.yml
index af0387de..9db6642d 100644
--- a/tests/end_to_end/repo/.github/workflows/coverage-comment.yml
+++ b/tests/end_to_end/repo/.github/workflows/coverage-comment.yml
@@ -21,3 +21,4 @@ jobs:
         with:
           GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           GITHUB_PR_RUN_ID: ${{ github.event.workflow_run.id }}
+          COVERAGE_PATH: __ACTION_COVERAGE_PATH__
diff --git a/tests/end_to_end/test_all.py b/tests/end_to_end/test_all.py
index 81482cb0..4b445295 100644
--- a/tests/end_to_end/test_all.py
+++ b/tests/end_to_end/test_all.py
@@ -5,6 +5,7 @@
 
 
 @pytest.mark.repo_suffix("public")
+@pytest.mark.code_path("subdir")
 def test_public_repo(
     gh_create_repo,
     wait_for_run_to_start,
@@ -28,7 +29,7 @@ def test_public_repo(
     run_id = wait_for_run_to_start(sha1=get_sha1(), branch="main", gh=gh_me)
 
     # AAAaand it's started. Now let's wait for it to end.
-    # Also, raise if it doesn't end succefully. That half of the job.
+    # Also, raise if it doesn't end successfully. That half of the job.
     gh_me("run", "watch", run_id, "--exit-status")
 
     # Now to the other half: maybe it did nothing successfully, so let's check