diff --git a/scripts/codex-maintenance.sh b/scripts/codex-maintenance.sh
index 26827ba..7cbe636 100755
--- a/scripts/codex-maintenance.sh
+++ b/scripts/codex-maintenance.sh
@@ -37,6 +37,17 @@ source "${script_dir}/lib/nix-parallel.sh"
 repo_root="$(cd "${script_dir}/.." && pwd)"
 cd "$repo_root"
 
+# When this repo is a subdirectory of a larger git repo (e.g. a mono-repo
+# subtree), `git diff --name-only` outputs paths relative to the outer git
+# root, not this directory. Compute a prefix to strip so pattern matching
+# below works correctly regardless of nesting depth.
+_git_root="$(git rev-parse --show-toplevel 2>/dev/null || echo "$repo_root")"
+if [[ "$repo_root" != "$_git_root" ]]; then
+  _subtree_prefix="${repo_root#"$_git_root"/}/"
+else
+  _subtree_prefix=""
+fi
+
 full_check=false
 dry_run=false
 
@@ -120,7 +131,7 @@ if ! $full_check; then
   base_ref="$(resolve_base_ref)"
   echo
   echo "Changed-files scope: diffing against ${base_ref}"
-  mapfile -t changed_files < <(git diff --name-only --diff-filter=ACMR "$base_ref" -- . | sort -u)
+  mapfile -t changed_files < <(git diff --name-only --diff-filter=ACMR "$base_ref" -- . | sort -u | sed "s|^${_subtree_prefix}||")
 
   if [[ ${#changed_files[@]} -eq 0 ]]; then
     echo "No changed files detected."