diff --git a/lib/Magento/App/Config.php b/lib/Magento/App/Config.php
index 0cfc5010902f1..0d454d143aa59 100644
--- a/lib/Magento/App/Config.php
+++ b/lib/Magento/App/Config.php
@@ -79,6 +79,9 @@ protected function _parseParams(array $input)
                     foreach ($value as $subKey => $node) {
                         $build[$key . $separator . $subKey] = $node;
                     }
+                    if(array_key_exists($key, $build)){
+                        unset($build[$key]);
+                    }
                 } else {
                     $build[$key] = null;
                 }