diff --git a/config/cli-config.php b/config/cli-config.php
index 52659e4e..1f211557 100644
--- a/config/cli-config.php
+++ b/config/cli-config.php
@@ -2,11 +2,29 @@
 
 declare(strict_types=1);
 
+use Doctrine\Migrations\Configuration\EntityManager\ExistingEntityManager;
+use Doctrine\Migrations\Configuration\Migration\ConfigurationArray;
+use Doctrine\Migrations\DependencyFactory;
 use Doctrine\ORM\EntityManager;
-use Doctrine\ORM\Tools\Console\ConsoleRunner;
+
+// This file is currently used by docrtrine migrations only
 
 return (static function () {
     /** @var EntityManager $em */
     $em = include __DIR__ . '/entity-manager.php';
-    return ConsoleRunner::createHelperSet($em);
+
+    $migrationsConfig = [
+        'migrations_paths' => [
+            'ShlinkMigrations' => 'data/migrations',
+        ],
+        'table_storage' => [
+            'table_name' => 'migrations',
+        ],
+        'custom_template' => 'data/migrations_template.txt',
+    ];
+
+    return DependencyFactory::fromEntityManager(
+        new ConfigurationArray($migrationsConfig),
+        new ExistingEntityManager($em),
+    );
 })();
diff --git a/migrations.php b/migrations.php
deleted file mode 100644
index 306c1c08..00000000
--- a/migrations.php
+++ /dev/null
@@ -1,15 +0,0 @@
-<?php
-
-declare(strict_types=1);
-
-return [
-
-    'migrations_paths' => [
-        'ShlinkMigrations' => 'data/migrations',
-    ],
-    'table_storage' => [
-        'table_name' => 'migrations',
-    ],
-    'custom_template' => 'data/migrations_template.txt',
-
-];