diff --git a/refs/files-backend.c b/refs/files-backend.c
index c11213f520..8953d1c6d3 100644
--- a/refs/files-backend.c
+++ b/refs/files-backend.c
@@ -2611,6 +2611,9 @@ static int lock_ref_for_update(struct files_ref_store *refs,
 
 	update->backend_data = lock;
 
+	if (update->flags & REF_LOG_ONLY)
+		goto out;
+
 	if (update->type & REF_ISSYMREF) {
 		if (update->flags & REF_NO_DEREF) {
 			/*
@@ -2829,13 +2832,16 @@ static int files_transaction_prepare(struct ref_store *ref_store,
 	 */
 	for (i = 0; i < transaction->nr; i++) {
 		struct ref_update *update = transaction->updates[i];
-		struct string_list_item *item =
-			string_list_append(&affected_refnames, update->refname);
+		struct string_list_item *item;
 
 		if ((update->flags & REF_IS_PRUNING) &&
 		    !(update->flags & REF_NO_DEREF))
 			BUG("REF_IS_PRUNING set without REF_NO_DEREF");
 
+		if (update->flags & REF_LOG_ONLY)
+			continue;
+
+		item = string_list_append(&affected_refnames, update->refname);
 		/*
 		 * We store a pointer to update in item->util, but at
 		 * the moment we never use the value of this field
@@ -3035,8 +3041,9 @@ static int files_transaction_finish_initial(struct files_ref_store *refs,
 
 	/* Fail if a refname appears more than once in the transaction: */
 	for (i = 0; i < transaction->nr; i++)
-		string_list_append(&affected_refnames,
-				   transaction->updates[i]->refname);
+		if (!(transaction->updates[i]->flags & REF_LOG_ONLY))
+			string_list_append(&affected_refnames,
+					   transaction->updates[i]->refname);
 	string_list_sort(&affected_refnames);
 	if (ref_update_reject_duplicates(&affected_refnames, err)) {
 		ret = TRANSACTION_GENERIC_ERROR;
diff --git a/refs/reftable-backend.c b/refs/reftable-backend.c
index b2e3ba877d..bec5962deb 100644
--- a/refs/reftable-backend.c
+++ b/refs/reftable-backend.c
@@ -990,8 +990,9 @@ static int reftable_be_transaction_prepare(struct ref_store *ref_store,
 		if (ret)
 			goto done;
 
-		string_list_append(&affected_refnames,
-				   transaction->updates[i]->refname);
+		if (!(transaction->updates[i]->flags & REF_LOG_ONLY))
+			string_list_append(&affected_refnames,
+					   transaction->updates[i]->refname);
 	}
 
 	/*
@@ -1301,6 +1302,7 @@ static int write_transaction_table(struct reftable_writer *writer, void *cb_data
 	struct reftable_log_record *logs = NULL;
 	struct ident_split committer_ident = {0};
 	size_t logs_nr = 0, logs_alloc = 0, i;
+	uint64_t max_update_index = ts;
 	const char *committer_info;
 	int ret = 0;
 
@@ -1405,7 +1407,19 @@ static int write_transaction_table(struct reftable_writer *writer, void *cb_data
 				}
 
 				fill_reftable_log_record(log, &c);
-				log->update_index = ts;
+
+				/*
+				 * Updates are sorted by the writer. So updates for the same
+				 * refname need to contain different update indices.
+				 */
+				log->update_index = ts + u->index;
+
+				/*
+				 * Note the max update_index so the limit can be set later on.
+				 */
+				if (log->update_index > max_update_index)
+					max_update_index = log->update_index;
+
 				log->refname = xstrdup(u->refname);
 				memcpy(log->value.update.new_hash,
 				       u->new_oid.hash, GIT_MAX_RAWSZ);
@@ -1469,6 +1483,8 @@ static int write_transaction_table(struct reftable_writer *writer, void *cb_data
 	 * and log blocks.
 	 */
 	if (logs) {
+		reftable_writer_set_limits(writer, ts, max_update_index);
+
 		ret = reftable_writer_add_logs(writer, logs, logs_nr);
 		if (ret < 0)
 			goto done;