diff --git a/tools/ci/init-submodules.sh b/tools/ci/init-submodules.sh
index 6a87d13..572311d 100755
--- a/tools/ci/init-submodules.sh
+++ b/tools/ci/init-submodules.sh
@@ -25,7 +25,11 @@ fi
   git submodule update --init --recursive --jobs 4 >/tmp/ghost_sub_init.log 2>&1 || true
 
   while IFS= read -r path; do
-    if [ ! -d "$path" ] || [ -z "$(ls -A "$path" 2>/dev/null)" ]; then
+    # A submodule needs self-healing when it has no .git, or its worktree
+    # has no files other than the .git pointer (ls -A counts .git and would
+    # wrongly treat an un-checked-out submodule as initialized).
+    if [ ! -e "$path/.git" ] ||
+       [ -z "$(find "$path" -mindepth 1 -maxdepth 1 ! -name '.git' -print -quit 2>/dev/null)" ]; then
       echo "init-submodules: self-healing empty submodule $path"
       if (cd "$path" && git fetch --depth 1 origin >/dev/null 2>&1 &&
           git checkout -q FETCH_HEAD >/dev/null 2>&1); then