diff --git a/builtin/clone.c b/builtin/clone.c
index ec2f75b4f3..8d23a62e8a 100644
--- a/builtin/clone.c
+++ b/builtin/clone.c
@@ -771,8 +771,10 @@ int cmd_clone(int argc, const char **argv, const char *prefix)
 		die(_("could not create leading directories of '%s'"), git_dir);
 
 	set_git_dir_init(git_dir, real_git_dir, 0);
-	if (real_git_dir)
+	if (real_git_dir) {
 		git_dir = real_git_dir;
+		junk_git_dir = real_git_dir;
+	}
 
 	if (0 <= option_verbosity) {
 		if (option_bare)
diff --git a/t/t5600-clone-fail-cleanup.sh b/t/t5600-clone-fail-cleanup.sh
index ee06d28649..4435693bb2 100755
--- a/t/t5600-clone-fail-cleanup.sh
+++ b/t/t5600-clone-fail-cleanup.sh
@@ -37,6 +37,16 @@ test_expect_success \
 
 test_expect_success \
     'successful clone must leave the directory' \
-    'cd bar'
+    'test -d bar'
+
+test_expect_success 'failed clone --separate-git-dir should not leave any directories' '
+	mkdir foo/.git/objects.bak/ &&
+	mv foo/.git/objects/* foo/.git/objects.bak/ &&
+	test_must_fail git clone --separate-git-dir gitdir foo worktree &&
+	test_must_fail test -e gitdir &&
+	test_must_fail test -e worktree &&
+	mv foo/.git/objects.bak/* foo/.git/objects/ &&
+	rmdir foo/.git/objects.bak
+'
 
 test_done