diff --git a/wp-admin/options-permalink.php b/wp-admin/options-permalink.php
index 88947b9110..55a0cc2304 100644
--- a/wp-admin/options-permalink.php
+++ b/wp-admin/options-permalink.php
@@ -160,7 +160,7 @@ $using_index_permalinks = $wp_rewrite->using_index_permalinks();
 if ( $structure_updated ) {
 	$message = __( 'Permalink structure updated.' );
 
-	if ( $permalink_structure && ! $using_index_permalinks ) {
+	if ( ! is_multisite() && $permalink_structure && ! $using_index_permalinks ) {
 		if ( $iis7_permalinks ) {
 			if ( ! $writable ) {
 				$message = sprintf(
diff --git a/wp-includes/version.php b/wp-includes/version.php
index 4a40c6ce2e..32a994a3bb 100644
--- a/wp-includes/version.php
+++ b/wp-includes/version.php
@@ -13,7 +13,7 @@
  *
  * @global string $wp_version
  */
-$wp_version = '5.6-alpha-48712';
+$wp_version = '5.6-alpha-48713';
 
 /**
  * Holds the WordPress DB revision, increments when changes are made to the WordPress DB schema.