diff -u b/core/lib/Drupal/Core/Config/Entity/ConfigStorageController.php b/core/lib/Drupal/Core/Config/Entity/ConfigStorageController.php
--- b/core/lib/Drupal/Core/Config/Entity/ConfigStorageController.php
+++ b/core/lib/Drupal/Core/Config/Entity/ConfigStorageController.php
@@ -269,7 +269,9 @@
       $config = config($this->getConfigPrefix() . $entity->id());
       $config->delete();
 
-      // Remove the entity from the manifest file.
+      // Remove the entity from the manifest file. Entity id's can contain a dot
+      // so we can not use Config::clear() to remove the entity from the
+      // manifest.
       $manifest = config('manifest.' . $this->entityInfo['config_prefix']);
       $manifest_data = $manifest->get();
       unset($manifest_data[$entity->id()]);
reverted:
--- b/core/modules/config/lib/Drupal/config/Tests/ConfigImportUITest.php
+++ a/core/modules/config/lib/Drupal/config/Tests/ConfigImportUITest.php
@@ -128,5 +128,4 @@
     $config_data['name'] = $new_site_name;
     $staging->write('system.site', $config_data);
   }
-
 }
diff -u /dev/null b/core/modules/config/tests/config_test/config/config_test.dynamic.test.config.yml
--- /dev/null
+++ b/core/modules/config/tests/config_test/config/config_test.dynamic.test.config.yml
@@ -1 +1,3 @@
+id: test.config
+label: Default
 protected_property: Default
reverted:
--- b/core/modules/config/tests/config_test/config/config_test.dynamic.test.config.yml
+++ /dev/null
@@ -1,2 +0,0 @@
-id: test.config
-label: Default