diff --git a/setup.c b/setup.c
index 8a488f3e7c..53ffeabc5b 100644
--- a/setup.c
+++ b/setup.c
@@ -2534,7 +2534,9 @@ static void repository_format_configure(struct repository_format *repo_fmt,
 		ref_format = ref_storage_format_by_name(env);
 		if (ref_format == REF_STORAGE_FORMAT_UNKNOWN)
 			die(_("unknown ref storage format '%s'"), env);
-		repo_fmt->ref_storage_format = ref_format;
+		if (repo_fmt->version < 0 ||
+		    repo_fmt->ref_storage_format == REF_STORAGE_FORMAT_UNKNOWN)
+			repo_fmt->ref_storage_format = ref_format;
 	} else if (cfg.ref_format != REF_STORAGE_FORMAT_UNKNOWN) {
 		repo_fmt->ref_storage_format = cfg.ref_format;
 	}
diff --git a/t/t0001-init.sh b/t/t0001-init.sh
index 213d5984b1..6dff8b75f1 100755
--- a/t/t0001-init.sh
+++ b/t/t0001-init.sh
@@ -697,6 +697,15 @@ do
 		git -C refformat rev-parse --show-ref-format >actual &&
 		test_cmp expect actual
 	'
+
+	test_expect_success "reinit repository with GIT_DEFAULT_REF_FORMAT=$format does not change format" '
+		test_when_finished "rm -rf refformat" &&
+		git init refformat &&
+		git -C refformat rev-parse --show-ref-format >expect &&
+		GIT_DEFAULT_REF_FORMAT=$format git init refformat &&
+		git -C refformat rev-parse --show-ref-format >actual &&
+		test_cmp expect actual
+	'
 done
 
 test_expect_success "--ref-format= overrides GIT_DEFAULT_REF_FORMAT" '