diff --git a/setup.c b/setup.c
index 65fe5ecefb..019a1c6367 100644
--- a/setup.c
+++ b/setup.c
@@ -1273,6 +1273,7 @@ void check_repository_format(struct repository_format *fmt)
 		fmt = &repo_fmt;
 	check_repository_format_gently(get_git_dir(), fmt, NULL);
 	startup_info->have_repository = 1;
+	repo_set_hash_algo(the_repository, fmt->hash_algo);
 	clear_repository_format(&repo_fmt);
 }