diff -u b/core/modules/filter/src/Entity/FilterFormat.php b/core/modules/filter/src/Entity/FilterFormat.php
--- b/core/modules/filter/src/Entity/FilterFormat.php
+++ b/core/modules/filter/src/Entity/FilterFormat.php
@@ -7,6 +7,7 @@
 
 namespace Drupal\filter\Entity;
 
+use Drupal\Component\Plugin\PluginInspectionInterface;
 use Drupal\Core\Config\Entity\ConfigEntityBase;
 use Drupal\Core\Entity\EntityWithPluginCollectionInterface;
 use Drupal\Core\Entity\EntityStorageInterface;
@@ -414,2 +415,15 @@
 
+  /**
+   * {@inheritdoc}
+   */
+  protected function calculatePluginDependencies(PluginInspectionInterface $instance) {
+    // Only add dependencies for plugins that are actually configured. This is
+    // necessary because the filter plugin collection will return all available
+    // filter plugins.
+    // @see \Drupal\filter\FilterPluginCollection::getConfiguration()
+    if (isset($this->filters[$instance->getPluginId()])) {
+      parent::calculatePluginDependencies($instance);
+    }
+  }
+
 }
diff -u b/core/modules/filter/src/Tests/FilterAPITest.php b/core/modules/filter/src/Tests/FilterAPITest.php
--- b/core/modules/filter/src/Tests/FilterAPITest.php
+++ b/core/modules/filter/src/Tests/FilterAPITest.php
@@ -395,14 +395,18 @@
    */
   public function testDependencyRemoval() {
-    $filter_format = entity_load('filter_format', 'filtered_html');
-    $filter_config = array(
+    $this->installSchema('user', array('users_data'));
+    $filter_format = \Drupal\filter\Entity\FilterFormat::load('filtered_html');
+    $filter_config = [
       'weight' => 10,
       'status' => 1,
-    );
+    ];
     $filter_format->setFilterConfig('filter_test_restrict_tags_and_attributes', $filter_config);
     $filter_format->save();
-    $this->uninstallModule('filter_test');
-    $filter_format = entity_load('filter_format', 'filtered_html');
-    $this->assertEqual('Drupal\filter\Entity\FilterFormat', get_class($filter_format));
+    $this->assertEqual(['module' => ['filter_test']], $filter_format->getDependencies());
+    \Drupal::moduleHandler()->uninstall(array('filter_test'));
+
+    \Drupal::entityManager()->getStorage('filter_format')->resetCache();
+    $filter_format = \Drupal\filter\Entity\FilterFormat::load('filtered_html');
+    $this->assertEqual([], $filter_format->getDependencies());
   }
 }