diff --git a/Documentation/git-clean.txt b/Documentation/git-clean.txt
index 3ab749b921..ba31d8d166 100644
--- a/Documentation/git-clean.txt
+++ b/Documentation/git-clean.txt
@@ -37,9 +37,9 @@ OPTIONS
 --force::
 	If the Git configuration variable clean.requireForce is not set
 	to false, 'git clean' will refuse to delete files or directories
-	unless given -f or -i. Git will refuse to delete directories
-	with .git sub directory or file unless a second -f
-	is given.
+	unless given -f or -i.  Git will refuse to modify untracked
+	nested git repositories (directories with a .git subdirectory)
+	unless a second -f is given.
 
 -i::
 --interactive::
diff --git a/builtin/clean.c b/builtin/clean.c
index 68d70e41c0..3a7a63ae71 100644
--- a/builtin/clean.c
+++ b/builtin/clean.c
@@ -946,6 +946,8 @@ int cmd_clean(int argc, const char **argv, const char *prefix)
 
 	if (force > 1)
 		rm_flags = 0;
+	else
+		dir.flags |= DIR_SKIP_NESTED_GIT;
 
 	dir.flags |= DIR_SHOW_OTHER_DIRECTORIES;
 
diff --git a/dir.c b/dir.c
index 3b2fe1701c..7ff79170fc 100644
--- a/dir.c
+++ b/dir.c
@@ -1451,6 +1451,16 @@ static enum path_treatment treat_directory(struct dir_struct *dir,
 		return path_none;
 
 	case index_nonexistent:
+		if (dir->flags & DIR_SKIP_NESTED_GIT) {
+			int nested_repo;
+			struct strbuf sb = STRBUF_INIT;
+			strbuf_addstr(&sb, dirname);
+			nested_repo = is_nonbare_repository_dir(&sb);
+			strbuf_release(&sb);
+			if (nested_repo)
+				return path_none;
+		}
+
 		if (dir->flags & DIR_SHOW_OTHER_DIRECTORIES)
 			break;
 		if (exclude &&
diff --git a/dir.h b/dir.h
index 46c238ab49..739aea7c96 100644
--- a/dir.h
+++ b/dir.h
@@ -156,7 +156,8 @@ struct dir_struct {
 		DIR_SHOW_IGNORED_TOO = 1<<5,
 		DIR_COLLECT_KILLED_ONLY = 1<<6,
 		DIR_KEEP_UNTRACKED_CONTENTS = 1<<7,
-		DIR_SHOW_IGNORED_TOO_MODE_MATCHING = 1<<8
+		DIR_SHOW_IGNORED_TOO_MODE_MATCHING = 1<<8,
+		DIR_SKIP_NESTED_GIT = 1<<9
 	} flags;
 	struct dir_entry **entries;
 	struct dir_entry **ignored;
diff --git a/t/t7300-clean.sh b/t/t7300-clean.sh
index 530dfdab34..6e6d24c1c3 100755
--- a/t/t7300-clean.sh
+++ b/t/t7300-clean.sh
@@ -549,7 +549,7 @@ test_expect_failure 'nested (non-empty) bare repositories should be cleaned even
 	test_path_is_missing strange_bare
 '
 
-test_expect_success 'giving path in nested git work tree will remove it' '
+test_expect_success 'giving path in nested git work tree will NOT remove it' '
 	rm -fr repo &&
 	mkdir repo &&
 	(
@@ -561,7 +561,7 @@ test_expect_success 'giving path in nested git work tree will remove it' '
 	git clean -f -d repo/bar/baz &&
 	test_path_is_file repo/.git/HEAD &&
 	test_path_is_dir repo/bar/ &&
-	test_path_is_missing repo/bar/baz
+	test_path_is_file repo/bar/baz/hello.world
 '
 
 test_expect_success 'giving path to nested .git will not remove it' '
@@ -579,7 +579,7 @@ test_expect_success 'giving path to nested .git will not remove it' '
 	test_path_is_dir untracked/
 '
 
-test_expect_success 'giving path to nested .git/ will remove contents' '
+test_expect_success 'giving path to nested .git/ will NOT remove contents' '
 	rm -fr repo untracked &&
 	mkdir repo untracked &&
 	(
@@ -589,7 +589,7 @@ test_expect_success 'giving path to nested .git/ will remove contents' '
 	) &&
 	git clean -f -d repo/.git/ &&
 	test_path_is_dir repo/.git &&
-	test_dir_is_empty repo/.git &&
+	test_path_is_file repo/.git/HEAD &&
 	test_path_is_dir untracked/
 '
 
@@ -671,7 +671,7 @@ test_expect_success 'git clean -d skips untracked dirs containing ignored files'
 	test_path_is_missing foo/b/bb
 '
 
-test_expect_failure 'git clean -d skips nested repo containing ignored files' '
+test_expect_success 'git clean -d skips nested repo containing ignored files' '
 	test_when_finished "rm -rf nested-repo-with-ignored-file" &&
 
 	git init nested-repo-with-ignored-file &&