diff -u b/core/lib/Drupal/Core/Config/Config.php b/core/lib/Drupal/Core/Config/Config.php
--- b/core/lib/Drupal/Core/Config/Config.php
+++ b/core/lib/Drupal/Core/Config/Config.php
@@ -190,6 +190,8 @@
    */
   public function setData(array $data) {
     $this->data = $data;
+    // When importing new config, a load would destroy the data just set.
+    $this->isLoaded = TRUE;
     $this->resetOverriddenData();
     return $this;
   }