diff --git a/plugins/disk-cleanup/disk_cleanup.py b/plugins/disk-cleanup/disk_cleanup.py
index cef2698316..5cdb294cd2 100755
--- a/plugins/disk-cleanup/disk_cleanup.py
+++ b/plugins/disk-cleanup/disk_cleanup.py
@@ -10,7 +10,7 @@ Rules:
   - test files    → delete immediately at task end (age >= 0)
   - temp files    → delete after 7 days
   - cron-output   → delete after 14 days
-  - empty dirs    → always delete (under HERMES_HOME)
+  - empty dirs    → delete when safe under HERMES_HOME (excluding checkpoint shadow-repo dirs and git internals)
   - research      → keep 10 newest, prompt for older (deep only)
   - chrome-profile→ prompt after 14 days (deep only)
   - >500 MB files → prompt always (deep only)
@@ -145,6 +145,29 @@ ALLOWED_CATEGORIES = {
 }
 
 
+def _is_protected_empty_dir(dirpath: Path, hermes_home: Path) -> bool:
+    """Return True when an empty-dir cleanup candidate must be preserved.
+
+    This protects git internals for both Hermes checkpoint shadow repos
+    (stored under ``checkpoints/<id>/...``) and ordinary repos living under
+    ``HERMES_HOME`` (stored under ``.git/...``).
+    """
+    try:
+        rel_parts = dirpath.relative_to(hermes_home).parts
+    except ValueError:
+        return False
+
+    if ".git" in rel_parts and rel_parts[-1] != ".git":
+        return True
+
+    if len(rel_parts) >= 2 and rel_parts[0] == "checkpoints":
+        repo_root = hermes_home / rel_parts[0] / rel_parts[1]
+        if any((repo_root / marker).exists() for marker in ("HEAD", "HERMES_WORKDIR", "config")):
+            return True
+
+    return False
+
+
 def fmt_size(n: float) -> str:
     for unit in ("B", "KB", "MB", "GB", "TB"):
         if n < 1024:
@@ -309,6 +332,8 @@ def quick() -> Dict[str, Any]:
                 rel_parts = dirpath.relative_to(hermes_home).parts
             except ValueError:
                 continue
+            if _is_protected_empty_dir(dirpath, hermes_home):
+                continue
             # Skip the well-known top-level state dirs themselves.
             if len(rel_parts) == 1 and rel_parts[0] in _PROTECTED_TOP_LEVEL:
                 continue
diff --git a/tests/plugins/test_disk_cleanup_plugin.py b/tests/plugins/test_disk_cleanup_plugin.py
index e1463bced7..bbaace74a8 100644
--- a/tests/plugins/test_disk_cleanup_plugin.py
+++ b/tests/plugins/test_disk_cleanup_plugin.py
@@ -195,6 +195,28 @@ class TestTrackForgetQuick:
         for d in ("logs", "memories", "sessions", "cron", "cache"):
             assert (_isolate_env / d).exists(), f"{d}/ should be preserved"
 
+    def test_quick_preserves_git_internal_dirs_and_removes_normal_empty_dirs(self, _isolate_env):
+        dg = _load_lib()
+        checkpoint_heads = _isolate_env / "checkpoints" / "demo" / "refs" / "heads"
+        checkpoint_info = _isolate_env / "checkpoints" / "demo" / "objects" / "info"
+        repo_heads = _isolate_env / "scratch" / "repo" / ".git" / "refs" / "heads"
+        repo_info = _isolate_env / "scratch" / "repo" / ".git" / "objects" / "info"
+        plain_empty = _isolate_env / "scratch" / "empty-dir"
+
+        for p in (checkpoint_heads, checkpoint_info, repo_heads, repo_info):
+            p.mkdir(parents=True, exist_ok=True)
+        (_isolate_env / "checkpoints" / "demo" / "HERMES_WORKDIR").write_text("/tmp/demo\n")
+        plain_empty.mkdir(parents=True)
+
+        summary = dg.quick()
+
+        assert checkpoint_heads.exists()
+        assert checkpoint_info.exists()
+        assert repo_heads.exists()
+        assert repo_info.exists()
+        assert not plain_empty.exists()
+        assert summary["empty_dirs"] == 1
+
 
 class TestStatus:
     def test_empty_status(self, _isolate_env):