diff -u b/admin_toolbar_tools/src/ToolbarHandler.php b/admin_toolbar_tools/src/ToolbarHandler.php
--- b/admin_toolbar_tools/src/ToolbarHandler.php
+++ b/admin_toolbar_tools/src/ToolbarHandler.php
@@ -16,7 +16,6 @@
 
   use StringTranslationTrait;
 
-
   /**
    * The module service.
    *
@@ -57,30 +56,50 @@
     // Core toolbar module calculates cachability in advance so we have to build
     // a fake menu tree here, including access checks.
     $tools_menu = &$build['administration_menu']['#items']['admin_toolbar_tools.help']['below'];
-    $tools_menu += $this->createMenuRenderArray('system.run_cron', 'Run cron');
-    $tools_menu += $this->createMenuRenderArray('admin_toolbar_tools.flush', 'Flush all caches', TRUE);
-    if (isset($tools_menu['admin_toolbar_tools.flush']['below'])) {
-      $tools_sub_menu = &$tools_menu['admin_toolbar_tools.flush']['below'];
-      $tools_sub_menu += $this->createMenuRenderArray('admin_toolbar_tools.cssjs', 'Flush CSS and Javascript');
-      $tools_sub_menu += $this->createMenuRenderArray('admin_toolbar_tools.plugin', 'Flush plugins cache');
-      $tools_sub_menu += $this->createMenuRenderArray('admin_toolbar_tools.flush_static', 'Flush static cache');
-      $tools_sub_menu += $this->createMenuRenderArray('admin_toolbar_tools.flush_menu', 'Flush routing and links  cache');
-      $tools_sub_menu += $this->createMenuRenderArray('admin_toolbar_tools.flush_rendercache', 'Flush render cache');
-
-      // Adding a menu link to clean the Views cache.
-      if ($this->moduleHandler->moduleExists('views')) {
-        $tools_sub_menu += $this->createMenuRenderArray('admin_toolbar_tools.flush_views', 'Flush views cache');
-      }
+
+    // Adding the 'Flush all caches' menu in the correct place.
+    $menu_render_array = $this->createMenuRenderArray('admin_toolbar_tools.flush', $this->t('Flush all caches'), TRUE);
+    $this->arrayInsert($tools_menu, 1, $menu_render_array);
+
+    // Adding the submenus to 'Flush all caches' menu.
+    $tools_sub_menu = &$tools_menu['admin_toolbar_tools.flush']['below'];
+    $tools_sub_menu += $this->createMenuRenderArray('admin_toolbar_tools.cssjs', $this->t('Flush CSS and Javascript'));
+    $tools_sub_menu += $this->createMenuRenderArray('admin_toolbar_tools.plugin', $this->t('Flush plugins cache'));
+    $tools_sub_menu += $this->createMenuRenderArray('admin_toolbar_tools.flush_static', $this->t('Flush static cache'));
+    $tools_sub_menu += $this->createMenuRenderArray('admin_toolbar_tools.flush_menu', $this->t('Flush routing and links  cache'));
+    $tools_sub_menu += $this->createMenuRenderArray('admin_toolbar_tools.flush_rendercache', $this->t('Flush render cache'));
+
+    // Adding a menu link to clean the Views cache.
+    if ($this->moduleHandler->moduleExists('views')) {
+      $tools_sub_menu += $this->createMenuRenderArray('admin_toolbar_tools.flush_views', $this->t('Flush views cache'));
     }
+
+    // Adding the 'Run Cron' menu in the correct place.
+    $menu_render_array = $this->createMenuRenderArray('system.run_cron', $this->t('Run cron'));
+    $this->arrayInsert($tools_menu, 3, $menu_render_array);
+
     return $build;
   }
 
+  /**
+   * Create the menu render array.
+   *
+   * @param string $route
+   *    The route.
+   * @param string $title
+   *    The menu title.
+   * @param bool $submenu
+   *    Specify if the current menu element have a submenu.
+   *
+   * @return array
+   *   A renderable array as expected by the renderer service.
+   */
   private function createMenuRenderArray($route, $title, $submenu = FALSE) {
     $data = [];
     $url = Url::fromRoute($route);
     if ($url->access()) {
       $data[$route] = [
-        'title' => $this->t($title),
+        'title' => $title,
         'url' => $url,
         'attributes' => new Attribute(['class' => ['menu-item'] + ($submenu ? ['menu-item--expanded'] : [])]),
       ];
@@ -94,2 +113,21 @@
 
+  /**
+   * Insert an array in a given position of another array.
+   *
+   * @param array $array
+   *    The array where we need to insert new elements.
+   * @param int $position
+   *    The position where we will add the new array.
+   * @param array $insert_array
+   *    The array that will be inserted.
+   *
+   * @see http://php.net/manual/en/function.array-splice.php#56794
+   */
+  private function arrayInsert(array &$array, $position, array $insert_array) {
+    // Getting the first part of the array.
+    $first_array = array_splice($array, 0, $position);
+    // Inserting the new part in the desired position.
+    $array = array_merge($first_array, $insert_array, $array);
+  }
+
 }