diff -u b/core/includes/update.inc b/core/includes/update.inc
--- b/core/includes/update.inc
+++ b/core/includes/update.inc
@@ -618,14 +618,23 @@
       }
     }
   }
-  // Find update functions without edges to the system update and add such
-  // updates as edges to the system update as they have to be executed after the
-  // system update.
+  // Find update functions without edges to system updates and add such updates
+  // as edges to system updates so that system updates are executed first.
   foreach ($graph as $system_function => &$system_data) {
     if ($system_data['module'] === 'system') {
       foreach ($graph as $non_system_function => $non_system_data) {
-        if (($non_system_data['module'] !== 'system') && !isset($non_system_data['edges'][$system_function])) {
-          $system_data['edges'][$non_system_function] = TRUE;
+        if ($non_system_data['module'] !== 'system') {
+          $contains_system_update_edge = FALSE;
+          $edges = empty($non_system_data['edges']) ? [] : array_keys($non_system_data['edges']);
+          foreach ($edges as $edge) {
+            if ($graph[$edge]['module'] === 'system') {
+              $contains_system_update_edge = TRUE;
+              break;
+            }
+          }
+          if (!$contains_system_update_edge) {
+            $system_data['edges'][$non_system_function] = TRUE;
+          }
         }
       }
     }