diff --git a/setup/src/Magento/Setup/Model/Installer.php b/setup/src/Magento/Setup/Model/Installer.php
index a7dc4dd1e6099..9e3e64a62562e 100644
--- a/setup/src/Magento/Setup/Model/Installer.php
+++ b/setup/src/Magento/Setup/Model/Installer.php
@@ -432,12 +432,12 @@ private function createModulesConfig($request, $dryRun = false)
             } else {
                 $result[$module] = 1;
             }
-            if (in_array($module, $disable)) {
-                $result[$module] = 0;
-            }
             if (in_array($module, $enable)) {
                 $result[$module] = 1;
             }
+            if (in_array($module, $disable)) {
+                $result[$module] = 0;
+            }
         }
         if (!$dryRun) {
             $this->deploymentConfigWriter->saveConfig([ConfigFilePool::APP_CONFIG => ['modules' => $result]], true);