diff -u b/core/includes/install.core.inc b/core/includes/install.core.inc
--- b/core/includes/install.core.inc
+++ b/core/includes/install.core.inc
@@ -412,16 +412,6 @@
   // accessing the database before it is set up yet.)
   drupal_maintenance_theme();
 
-  // Ensure that the active configuration directory is empty if it is
-  // configured.
-  if ($install_state['config_verified']) {
-    $config = glob(config_get_config_directory(CONFIG_ACTIVE_DIRECTORY) . '/*.' . FileStorage::getFileExtension());
-    if (!empty($config)) {
-      $task = NULL;
-      throw new Exception(install_already_done_error());
-    }
-  }
-
   if ($install_state['database_verified']) {
     // Initialize the database system. Note that the connection
     // won't be initialized until it is actually requested.
@@ -439,6 +429,16 @@
     }
   }
 
+  // Ensure that the active configuration directory is empty before installation
+  // starts.
+  if ($install_state['config_verified'] && empty($task)) {
+    $config = glob(config_get_config_directory(CONFIG_ACTIVE_DIRECTORY) . '/*.' . FileStorage::getFileExtension());
+    if (!empty($config)) {
+      $task = NULL;
+      throw new Exception(install_already_done_error());
+    }
+  }
+
   // Modify the installation state as appropriate.
   $install_state['completed_task'] = $task;
   $install_state['database_tables_exist'] = !empty($task);