diff --git a/refs/files-backend.c b/refs/files-backend.c
index bf6f89b1d1938b6fae0c4125839c188b0d65fc86..00128f2183251e4b1170a8ce41b3d850202fb741 100644
--- a/refs/files-backend.c
+++ b/refs/files-backend.c
@@ -2760,6 +2760,8 @@ static void files_transaction_cleanup(struct files_ref_store *refs,
 
 		if (lock) {
 			unlock_ref(lock);
+			try_remove_empty_parents(refs, update->refname,
+						 REMOVE_EMPTY_PARENTS_REF);
 			update->backend_data = NULL;
 		}
 	}
diff --git a/t/t1400-update-ref.sh b/t/t1400-update-ref.sh
index e373d9108b651a0c7622a58aab515f212a06043b..c9893f65464f3b2a6585ed06c16beeed6a6a431b 100755
--- a/t/t1400-update-ref.sh
+++ b/t/t1400-update-ref.sh
@@ -2304,4 +2304,23 @@ test_expect_success 'update-ref should also create reflog for HEAD' '
 	test_cmp expect actual
 '
 
+test_expect_success REFFILES 'empty directories are pruned when aborting a transaction' '
+	test_path_is_missing .git/refs/heads/nested &&
+	git update-ref --stdin <<-EOF &&
+	create refs/heads/nested/something HEAD
+	prepare
+	abort
+	EOF
+	test_path_is_missing .git/refs/heads/nested
+'
+
+test_expect_success REFFILES 'empty directories are pruned when not committing' '
+	test_path_is_missing .git/refs/heads/nested &&
+	git update-ref --stdin <<-EOF &&
+	create refs/heads/nested/something HEAD
+	prepare
+	EOF
+	test_path_is_missing .git/refs/heads/nested
+'
+
 test_done