diff --git a/pkgs/clan-cli/clan_cli/dirs.py b/pkgs/clan-cli/clan_cli/dirs.py
index 064f52f..b3d5a2e 100644
--- a/pkgs/clan-cli/clan_cli/dirs.py
+++ b/pkgs/clan-cli/clan_cli/dirs.py
@@ -6,8 +6,16 @@ from .errors import ClanError
 
 
 def get_clan_flake_toplevel() -> Path:
+    return find_toplevel([".clan-flake", ".git", ".hg", ".svn", "flake.nix"])
+
+
+def find_git_repo_root() -> Path:
+    return find_toplevel([".git"])
+
+
+def find_toplevel(top_level_files: list[str]) -> Path:
     """Returns the path to the toplevel of the clan flake"""
-    for project_file in [".clan-flake", ".git", ".hg", ".svn", "flake.nix"]:
+    for project_file in top_level_files:
         initial_path = Path(os.getcwd())
         path = Path(initial_path)
         while path.parent != path:
diff --git a/pkgs/clan-cli/clan_cli/git.py b/pkgs/clan-cli/clan_cli/git.py
index bb2d7ce..700d0aa 100644
--- a/pkgs/clan-cli/clan_cli/git.py
+++ b/pkgs/clan-cli/clan_cli/git.py
@@ -2,7 +2,7 @@ import subprocess
 from pathlib import Path
 from typing import Optional
 
-from clan_cli.dirs import get_clan_flake_toplevel
+from clan_cli.dirs import find_git_repo_root
 from clan_cli.errors import ClanError
 from clan_cli.nix import nix_shell
 
@@ -15,7 +15,7 @@ def commit_file(
 ) -> None:
     # set default for repo_dir
     if repo_dir is None:
-        repo_dir = get_clan_flake_toplevel()
+        repo_dir = find_git_repo_root()
     # check that the file is in the git repository and exists
     if not Path(file_path).resolve().is_relative_to(repo_dir.resolve()):
         raise ClanError(f"File {file_path} is not in the git repository {repo_dir}")
@@ -43,7 +43,10 @@ def _commit_file_to_git(repo_dir: Path, file_path: Path, commit_message: str) ->
     # add the file to the git index
     subprocess.run(["git", "add", file_path], cwd=repo_dir, check=True)
     # commit only that file
-    cmd = nix_shell(["git"], ["git", "commit", "-m", commit_message, file_path.name])
+    cmd = nix_shell(
+        ["git"],
+        ["git", "commit", "-m", commit_message, str(file_path.relative_to(repo_dir))],
+    )
     subprocess.run(
         cmd,
         cwd=repo_dir,
diff --git a/pkgs/clan-cli/tests/test_git.py b/pkgs/clan-cli/tests/test_git.py
index 983dd60..fc69c7b 100644
--- a/pkgs/clan-cli/tests/test_git.py
+++ b/pkgs/clan-cli/tests/test_git.py
@@ -38,3 +38,30 @@ def test_commit_file_not_existing_raises_error(git_repo: Path) -> None:
     # commit a file that does not exist
     with pytest.raises(ClanError):
         git.commit_file(Path("test.txt"), git_repo, "test commit")
+
+
+def test_clan_flake_in_subdir(git_repo: Path, monkeypatch: pytest.MonkeyPatch) -> None:
+    # create a clan_flake subdirectory
+    (git_repo / "clan_flake").mkdir()
+    # create a .clan-flake file
+    (git_repo / "clan_flake" / ".clan-flake").touch()
+    # change to the clan_flake subdirectory
+    monkeypatch.chdir(git_repo / "clan_flake")
+    # commit files to git
+    subprocess.run(["git", "add", "."], cwd=git_repo)
+    subprocess.run(["git", "commit", "-m", "init"], cwd=git_repo)
+    # add a new file under ./clan_flake
+    (git_repo / "clan_flake" / "test.txt").touch()
+    # commit the file
+    git.commit_file(git_repo / "clan_flake" / "test.txt", git_repo, "test commit")
+    # check that the repo directory does in fact contain the file
+    assert (git_repo / "clan_flake" / "test.txt").exists()
+    # check that the working tree is clean
+    assert not subprocess.check_output(["git", "status", "--porcelain"], cwd=git_repo)
+    # check that the latest commit message is correct
+    assert (
+        subprocess.check_output(
+            ["git", "log", "-1", "--pretty=%B"], cwd=git_repo
+        ).decode("utf-8")
+        == "test commit\n\n"
+    )