diff --git a/cache.h b/cache.h
index 0f0485ecfe..e5885cc9ea 100644
--- a/cache.h
+++ b/cache.h
@@ -1042,6 +1042,7 @@ struct repository_format {
 	int worktree_config;
 	int is_bare;
 	int hash_algo;
+	int has_extensions;
 	char *work_tree;
 	struct string_list unknown_extensions;
 };
diff --git a/list-objects-filter-options.c b/list-objects-filter-options.c
index 256bcfbdfe..3553ad7b0a 100644
--- a/list-objects-filter-options.c
+++ b/list-objects-filter-options.c
@@ -326,7 +326,8 @@ void partial_clone_register(
 
 	/* Check if it is already registered */
 	if (!promisor_remote_find(remote)) {
-		git_config_set("core.repositoryformatversion", "1");
+		if (upgrade_repository_format(1) < 0)
+			die(_("unable to upgrade repository format to support partial clone"));
 
 		/* Add promisor config for the remote */
 		cfg_name = xstrfmt("remote.%s.promisor", remote);
diff --git a/repository.h b/repository.h
index 6534fbb7b3..3c1f7d54bd 100644
--- a/repository.h
+++ b/repository.h
@@ -196,4 +196,10 @@ void repo_update_index_if_able(struct repository *, struct lock_file *);
 
 void prepare_repo_settings(struct repository *r);
 
+/*
+ * Return 1 if upgrade repository format to target_version succeeded,
+ * 0 if no upgrade is necessary, and -1 when upgrade is not possible.
+ */
+int upgrade_repository_format(int target_version);
+
 #endif /* REPOSITORY_H */
diff --git a/setup.c b/setup.c
index 65fe5ecefb..597b41b822 100644
--- a/setup.c
+++ b/setup.c
@@ -455,6 +455,7 @@ static int check_repo_format(const char *var, const char *value, void *vdata)
 	if (strcmp(var, "core.repositoryformatversion") == 0)
 		data->version = git_config_int(var, value);
 	else if (skip_prefix(var, "extensions.", &ext)) {
+		data->has_extensions = 1;
 		/*
 		 * record any known extensions here; otherwise,
 		 * we fall through to recording it as unknown, and
@@ -538,6 +539,34 @@ static int check_repository_format_gently(const char *gitdir, struct repository_
 	return 0;
 }
 
+int upgrade_repository_format(int target_version)
+{
+	struct strbuf sb = STRBUF_INIT;
+	struct strbuf err = STRBUF_INIT;
+	struct strbuf repo_version = STRBUF_INIT;
+	struct repository_format repo_fmt = REPOSITORY_FORMAT_INIT;
+
+	strbuf_git_common_path(&sb, the_repository, "config");
+	read_repository_format(&repo_fmt, sb.buf);
+	strbuf_release(&sb);
+
+	if (repo_fmt.version >= target_version)
+		return 0;
+
+	if (verify_repository_format(&repo_fmt, &err) < 0 ||
+	    (!repo_fmt.version && repo_fmt.has_extensions)) {
+		warning("unable to upgrade repository format from %d to %d: %s",
+			repo_fmt.version, target_version, err.buf);
+		strbuf_release(&err);
+		return -1;
+	}
+
+	strbuf_addf(&repo_version, "%d", target_version);
+	git_config_set("core.repositoryformatversion", repo_version.buf);
+	strbuf_release(&repo_version);
+	return 1;
+}
+
 static void init_repository_format(struct repository_format *format)
 {
 	const struct repository_format fresh = REPOSITORY_FORMAT_INIT;