diff -u b/core/lib/Drupal/Core/Config/FileStorage.php b/core/lib/Drupal/Core/Config/FileStorage.php
--- b/core/lib/Drupal/Core/Config/FileStorage.php
+++ b/core/lib/Drupal/Core/Config/FileStorage.php
@@ -163,16 +163,7 @@
       }
       return FALSE;
     }
-    $success = drupal_unlink($this->getFilePath($name));
-
-    // If a collection is now empty remove the directory.
-    if ($success && $this->collection != StorageInterface::DEFAULT_COLLECTION) {
-      $names = $this->listAll();
-      if (empty($names)) {
-        drupal_rmdir($this->getCollectionDirectory());
-      }
-    }
-    return $success;
+    return drupal_unlink($this->getFilePath($name));
   }
 
   /**
@@ -238,7 +229,12 @@
         $success = FALSE;
       }
     }
-
+    if ($success && $this->collection != StorageInterface::DEFAULT_COLLECTION) {
+      // Remove empty directories.
+      if (!(new \FilesystemIterator($this->getCollectionDirectory()))->valid()) {
+        drupal_rmdir($this->getCollectionDirectory());
+      }
+    }
     return $success;
   }
 
@@ -310,9 +306,12 @@
             $collections[] = $collection . '.' . $sub_collection;
           }
         }
-        else {
-          // The directory has no subdirectories. Therefore add each directory
-          // to list of collections to be returned by the helper.
+        // Check that the collection is valid by searching if for configuration
+        // objects. A directory without any configuration objects is not a valid
+        // collection.
+        // \GlobIterator on Windows requires an absolute path.
+        $files = new \GlobIterator(realpath($directory . '/' . $collection) . '/*.' . $this->getFileExtension());
+        if (count($files)) {
           $collections[] = $collection;
         }
       }
diff -u b/core/lib/Drupal/Core/Config/StorageInterface.php b/core/lib/Drupal/Core/Config/StorageInterface.php
--- b/core/lib/Drupal/Core/Config/StorageInterface.php
+++ b/core/lib/Drupal/Core/Config/StorageInterface.php
@@ -176,13 +176,7 @@
    *   regex [a-zA-Z_.]. A storage does not need to have a collection set.
    *   However, if a collection is set, then storage should use it to store
    *   configuration in a way that allows retrieval of configuration for a
-   *   particular collection. Collections can be nested, for example
-   *   'language.de'. If this is a file system then we could create a language
-   *   folder with a subfolder named de. If this is a database table then there
-   *   could be a collection column which will store the value 'language.de'.
-   *   Storage nested levels should be consistent. If a collection with the name
-   *   'language.de' exists then a collections with the names 'language' or
-   *   'language.en.gb' should not be used.
+   *   particular collection.
    *
    * @return \Drupal\Core\Config\StorageInterface
    *   A new instance of the storage backend with the collection set.
diff -u b/core/modules/config/lib/Drupal/config/Tests/Storage/ConfigStorageTestBase.php b/core/modules/config/lib/Drupal/config/Tests/Storage/ConfigStorageTestBase.php
--- b/core/modules/config/lib/Drupal/config/Tests/Storage/ConfigStorageTestBase.php
+++ b/core/modules/config/lib/Drupal/config/Tests/Storage/ConfigStorageTestBase.php
@@ -232,6 +232,21 @@
     $alt_storage->delete($name);
     $this->assertIdentical(array('collection.sub.another', 'collection.sub.new'), $this->storage->getAllCollectionNames());
 
+    // Create configuration in collection called 'collection'. This ensures that
+    // FileStorage's collection storage works regardless of its use of
+    // subdirectories.
+    $parent_storage = $this->storage->createCollection('collection');
+    $this->assertFalse($parent_storage->exists($name));
+    $this->assertEqual(array(), $parent_storage->listAll());
+    $parent_storage->write($name, $new_data);
+    $this->assertIdentical($result, TRUE);
+    $this->assertIdentical($new_data, $parent_storage->read($name));
+    $this->assertEqual(array($name), $parent_storage->listAll());
+    $this->assertTrue($parent_storage->exists($name));
+    $this->assertIdentical(array('collection', 'collection.sub.another', 'collection.sub.new'), $this->storage->getAllCollectionNames());
+    $parent_storage->deleteAll();
+    $this->assertIdentical(array('collection.sub.another', 'collection.sub.new'), $this->storage->getAllCollectionNames());
+
     // Check that the having an empty collection-less storage does not break
     // anything. Before deleting check that the previous delete did not affect
     // data in another collection.