diff -u b/core/includes/module.inc b/core/includes/module.inc
--- b/core/includes/module.inc
+++ b/core/includes/module.inc
@@ -1176,13 +1176,17 @@
  */
 function module_set_weight($module, $weight) {
   $config = config('system.module');
-  $config_disabled = config('system.module.disabled');
+
+  // If the module is enabled it will be in the system.module config file.
   if ($config->get($module) !== NULL) {
     $config
       ->set($module, $weight)
       ->save('module_config_sort');
   }
-  elseif ($config_disabled->get($module) !== NULL) {
+  // Before writing to the system.module.disabled file ensure that the module
+  // has been previously enabled.
+  else if (drupal_container()->get('keyvalue')->get('system.module.schema')->get($module) !== FALSE) {
+    $config_disabled = config('system.module.disabled');
     // Only save non-zero weights to the system.module.disabled config file.
     if ($weight) {
       $config_disabled