diff --git a/builtin/clone.c b/builtin/clone.c
index 06966c5d4c25c5..fd052b8b543729 100644
--- a/builtin/clone.c
+++ b/builtin/clone.c
@@ -1097,8 +1097,14 @@ int cmd_clone(int argc, const char **argv, const char *prefix)
 		}
 	}
 
+	/*
+	 * Initialize the repository, but skip initializing the reference
+	 * database. We do not yet know about the object format of the
+	 * repository, and reference backends may persist that information into
+	 * their on-disk data structures.
+	 */
 	init_db(git_dir, real_git_dir, option_template, GIT_HASH_UNKNOWN, NULL,
-		do_not_override_repo_unix_permissions, INIT_DB_QUIET);
+		do_not_override_repo_unix_permissions, INIT_DB_QUIET | INIT_DB_SKIP_REFDB);
 
 	if (real_git_dir) {
 		free((char *)git_dir);
@@ -1282,6 +1288,7 @@ int cmd_clone(int argc, const char **argv, const char *prefix)
 	hash_algo = hash_algo_by_ptr(transport_get_hash_algo(transport));
 	initialize_repository_version(hash_algo, 1);
 	repo_set_hash_algo(the_repository, hash_algo);
+	create_reference_database(NULL, 1);
 
 	/*
 	 * Before fetching from the remote, download and install bundle
diff --git a/setup.c b/setup.c
index d6a1c59b7bd915..155fe13f701c7a 100644
--- a/setup.c
+++ b/setup.c
@@ -1897,7 +1897,7 @@ static int is_reinit(void)
 	return ret;
 }
 
-static void create_reference_database(const char *initial_branch, int quiet)
+void create_reference_database(const char *initial_branch, int quiet)
 {
 	struct strbuf err = STRBUF_INIT;
 	int reinit = is_reinit();
diff --git a/setup.h b/setup.h
index cbf538286bfefc..3f0f17c351cbc5 100644
--- a/setup.h
+++ b/setup.h
@@ -178,6 +178,7 @@ int init_db(const char *git_dir, const char *real_git_dir,
 	    const char *initial_branch, int init_shared_repository,
 	    unsigned int flags);
 void initialize_repository_version(int hash_algo, int reinit);
+void create_reference_database(const char *initial_branch, int quiet);
 
 /*
  * NOTE NOTE NOTE!!
diff --git a/t/t5550-http-fetch-dumb.sh b/t/t5550-http-fetch-dumb.sh
index e444b30bf61568..4c3b32785d580f 100755
--- a/t/t5550-http-fetch-dumb.sh
+++ b/t/t5550-http-fetch-dumb.sh
@@ -66,11 +66,11 @@ test_expect_success 'create empty remote repository' '
 	setup_post_update_server_info_hook "$HTTPD_DOCUMENT_ROOT_PATH/empty.git"
 '
 
-test_expect_success 'empty dumb HTTP repository has default hash algorithm' '
+test_expect_success 'empty dumb HTTP repository falls back to SHA1' '
 	test_when_finished "rm -fr clone-empty" &&
 	git clone $HTTPD_URL/dumb/empty.git clone-empty &&
 	git -C clone-empty rev-parse --show-object-format >empty-format &&
-	test "$(cat empty-format)" = "$(test_oid algo)"
+	test "$(cat empty-format)" = sha1
 '
 
 setup_askpass_helper