diff --git a/builtin/init-db.c b/builtin/init-db.c
index 6223b7d46af..da531f6b766 100644
--- a/builtin/init-db.c
+++ b/builtin/init-db.c
@@ -322,6 +322,7 @@ int set_git_dir_init(const char *git_dir, const char *real_git_dir,
 		set_git_dir(real_path(git_dir));
 		git_link = NULL;
 	}
+	startup_info->have_repository = 1;
 	return 0;
 }
 
diff --git a/setup.c b/setup.c
index fa7a306287a..3439ec6d815 100644
--- a/setup.c
+++ b/setup.c
@@ -986,7 +986,9 @@ int check_repository_format_version(const char *var, const char *value, void *cb
 
 int check_repository_format(void)
 {
-	return check_repository_format_gently(get_git_dir(), NULL);
+	check_repository_format_gently(get_git_dir(), NULL);
+	startup_info->have_repository = 1;
+	return 0;
 }
 
 /*