diff --git a/core/includes/install.inc b/core/includes/install.inc
index 1038818..d141656 100644
--- a/core/includes/install.inc
+++ b/core/includes/install.inc
@@ -466,18 +466,26 @@ function drupal_install_config_directories() {
 
   // Add a randomized config directory name to settings.php, unless it was
   // manually defined in the existing already.
-  if (empty($config_directories)) {
-    $config_directories_hash = Crypt::randomBytesBase64(55);
+  $settings = [];
+  $config_directories_hash = Crypt::randomBytesBase64(55);
+  if (empty($config_directories[CONFIG_ACTIVE_DIRECTORY])) {
     $settings['config_directories'] = array(
       CONFIG_ACTIVE_DIRECTORY => (object) array(
         'value' => conf_path() . '/files/config_' . $config_directories_hash . '/active',
         'required' => TRUE,
       ),
+    );
+  }
+  if (empty($config_directories[CONFIG_STAGING_DIRECTORY])) {
+    $settings['config_directories'] = array(
       CONFIG_STAGING_DIRECTORY => (object) array(
         'value' => conf_path() . '/files/config_' . $config_directories_hash . '/staging',
         'required' => TRUE,
       ),
     );
+  }
+
+  if ($settings) {
     // Rewrite settings.php, which also sets the value as global variable.
     drupal_rewrite_settings($settings);
   }
diff --git a/core/modules/system/system.install b/core/modules/system/system.install
index 108327a..842cbad 100644
--- a/core/modules/system/system.install
+++ b/core/modules/system/system.install
@@ -395,8 +395,9 @@ function system_requirements($phase) {
   // defined, the installer will create a valid config directory later, but
   // during runtime we must always display an error.
   if (!empty($GLOBALS['config_directories'])) {
-    $directories[] = config_get_config_directory(CONFIG_ACTIVE_DIRECTORY);
-    $directories[] = config_get_config_directory(CONFIG_STAGING_DIRECTORY);
+    foreach ($GLOBALS['config_directories'] as $type => $directory) {
+      $directories[] = config_get_config_directory($type);
+    }
   }
   elseif ($phase != 'install') {
     $requirements['config directories'] = array(