diff --git a/config/bootstrap.php b/config/bootstrap.php
index 5350d9dfd5..1911964ba8 100644
--- a/config/bootstrap.php
+++ b/config/bootstrap.php
@@ -197,21 +197,3 @@
 //Inflector::rules('irregular', ['red' => 'redlings']);
 //Inflector::rules('uninflected', ['dontinflectme']);
 //Inflector::rules('transliteration', ['/å/' => 'aa']);
-
-/*
- * Plugins need to be loaded manually, you can either load them one by one or all of them in a single call
- * Uncomment one of the lines below, as you need. make sure you read the documentation on Plugin to use more
- * advanced ways of loading plugins
- *
- * Plugin::loadAll(); // Loads all plugins at once
- * Plugin::load('Migrations'); //Loads a single plugin named Migrations
- *
- */
-
-/*
- * Only try to load DebugKit in development mode
- * Debug Kit should not be installed on a production system
- */
-if (Configure::read('debug')) {
-    Plugin::load('DebugKit', ['bootstrap' => true]);
-}
diff --git a/config/bootstrap_cli.php b/config/bootstrap_cli.php
index 85e119e9e1..287683a048 100644
--- a/config/bootstrap_cli.php
+++ b/config/bootstrap_cli.php
@@ -28,11 +28,3 @@
 // Set logs to different files so they don't have permission conflicts.
 Configure::write('Log.debug.file', 'cli-debug');
 Configure::write('Log.error.file', 'cli-error');
-
-try {
-    Plugin::load('Bake');
-} catch (MissingPluginException $e) {
-    // Do not halt if the plugin is missing
-}
-
-Plugin::load('Migrations');
diff --git a/src/Application.php b/src/Application.php
index 6f7c49d617..1ed4e143bc 100644
--- a/src/Application.php
+++ b/src/Application.php
@@ -36,6 +36,24 @@ public function bootstrap()
     {
         // Call parent to load bootstrap from files.
         parent::bootstrap();
+
+        if (PHP_SAPI === 'cli') {
+            try {
+                $this->addPlugin('Bake');
+            } catch (MissingPluginException $e) {
+                // Do not halt if the plugin is missing
+            }
+
+            $this->addPlugin('Migrations');
+        }
+
+        /*
+         * Only try to load DebugKit in development mode
+         * Debug Kit should not be installed on a production system
+         */
+        if (Configure::read('debug')) {
+            $this->addPlugin(\DebugKit\Plugin::class);
+        }
     }
 
     /**