diff -u b/core/includes/config.inc b/core/includes/config.inc
--- b/core/includes/config.inc
+++ b/core/includes/config.inc
@@ -29,6 +29,12 @@
     $source_storage = new FileStorage($config_dir);
     $target_storage = drupal_container()->get('config.storage');
 
+    // If this module defines any ConfigEntity types then create an empty
+    // manifest file for each of them.
+    foreach (config_get_module_config_entities($name) as $entity_info) {
+      config('manifest.' . $entity_info['config_prefix'])->save();
+    }
+
     $config_changes = array(
       'delete' => array(),
       'create' => array(),
diff -u b/core/modules/config/lib/Drupal/config/Tests/ConfigInstallTest.php b/core/modules/config/lib/Drupal/config/Tests/ConfigInstallTest.php
--- b/core/modules/config/lib/Drupal/config/Tests/ConfigInstallTest.php
+++ b/core/modules/config/lib/Drupal/config/Tests/ConfigInstallTest.php
@@ -36,15 +36,24 @@
     $default_config = 'config_test.system';
     $default_configuration_entity = 'config_test.dynamic.default';
     $default_config_manifest = 'manifest.config_test.dynamic';
+    $expected_manifest_data = array(
+      'default' => array(
+        'name' => 'config_test.dynamic.default',
+      ),
+    );
+    $default_empty_config_manifest = 'manifest.config_test.empty_manifest';
 
     // Verify that default module config does not exist before installation yet.
     $config = config($default_config);
     $this->assertIdentical($config->isNew(), TRUE);
     $config = config($default_configuration_entity);
     $this->assertIdentical($config->isNew(), TRUE);
-    // Verify that configuration entity manifest does not exist.
+
+    // Verify that configuration entity manifests do not exist.
     $config = config($default_config_manifest);
     $this->assertIdentical($config->isNew(), TRUE);
+    $config = config($default_empty_config_manifest);
+    $this->assertIdentical($config->isNew(), TRUE);
 
     // Install the test module.
     $this->enableModules(array('config_test'));
@@ -54,9 +63,13 @@
     $this->assertIdentical($config->isNew(), FALSE);
     $config = config($default_configuration_entity);
     $this->assertIdentical($config->isNew(), FALSE);
-    // Verify that configuration entity manifest has been created.
+
+    // Verify that configuration entity manifests have been created with
+    // expected contents.
     $config = config($default_config_manifest);
-    $this->assertIdentical($config->isNew(), FALSE);
+    $this->assertIdentical($config->get(), $expected_manifest_data);
+    $config = config($default_empty_config_manifest);
+    $this->assertIdentical($config->get(), array());
 
     // Verify that configuration import callback was invoked for the dynamic
     // configuration entity.
only in patch2:
unchanged:
--- /dev/null
+++ b/core/modules/config/tests/config_test/lib/Drupal/config_test/Plugin/Core/Entity/ConfigTestEmptyManifest.php
@@ -0,0 +1,53 @@
+<?php
+
+/**
+ * @file
+ * Definition of Drupal\config_test\Plugin\Core\Entity\ConfigTestEmptyManifest.
+ */
+
+namespace Drupal\config_test\Plugin\Core\Entity;
+
+use Drupal\Core\Config\Entity\ConfigEntityBase;
+use Drupal\Core\Annotation\Plugin;
+use Drupal\Core\Annotation\Translation;
+
+/**
+ * Defines the ConfigTestEmptyManifest configuration entity.
+ *
+ * @Plugin(
+ *   id = "config_test_empty_manifest",
+ *   label = @Translation("Test empty manifest creation"),
+ *   module = "config_test",
+ *   controller_class = "Drupal\config_test\ConfigTestStorageController",
+ *   config_prefix = "config_test.empty_manifest",
+ *   entity_keys = {
+ *     "id" = "id",
+ *     "label" = "label",
+ *     "uuid" = "uuid"
+ *   }
+ * )
+ */
+class ConfigTestEmptyManifest extends ConfigEntityBase {
+
+  /**
+   * The machine name for the configuration entity.
+   *
+   * @var string
+   */
+  public $id;
+
+  /**
+   * The UUID for the configuration entity.
+   *
+   * @var string
+   */
+  public $uuid;
+
+  /**
+   * The human-readable name of the configuration entity.
+   *
+   * @var string
+   */
+  public $label;
+
+}