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
@@ -403,7 +403,8 @@
     $changed = FALSE;
     $filters = $this->filters();
     foreach ($filters as $filter) {
-      if (in_array($filter->provider, $dependencies['module'])) {
+      // Only remove disabled filters.
+      if (!$filter->status && in_array($filter->provider, $dependencies['module'])) {
         $this->removeFilter($filter->getPluginId());
         $changed = TRUE;
       }
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
@@ -7,6 +7,7 @@
 
 namespace Drupal\filter\Tests;
 
+use Drupal\Component\Utility\String;
 use Drupal\Core\Session\AnonymousUserSession;
 use Drupal\Core\TypedData\OptionsProviderInterface;
 use Drupal\Core\TypedData\DataDefinition;
@@ -390,30 +391,60 @@
   /**
    * Tests that dependency removal works.
    *
-   * Uninstalling a module that provides a filter should not remove a text
-   * format that uses the filter.
+   * Uninstalling a module that provides a filter plugin should not remove a
+   * filter format configuration entity that does not have the filter plugin
+   * enabled.
    */
   public function testDependencyRemoval() {
     $this->installSchema('user', array('users_data'));
     $filter_format = \Drupal\filter\Entity\FilterFormat::load('filtered_html');
 
-    // Enable the filter_test_restrict_tags_and_attributes filter.
+    // Enable the filter_test_restrict_tags_and_attributes filter plugin on the
+    // filtered_html filter format.
     $filter_config = [
       'weight' => 10,
       'status' => 1,
     ];
     $filter_format->setFilterConfig('filter_test_restrict_tags_and_attributes', $filter_config)->save();
 
-    // Verify that a dependency exists on the module that provides the filter.
+    $module_data = _system_rebuild_module_data();
+    $this->assertTrue($module_data['filter_test']->info['required'], 'The filter_test module is required.');
+    $this->assertEqual($module_data['filter_test']->info['explanation'], String::format('Provides a filter plugin that is in use in the following filter formats: %formats', array('%formats' => $filter_format->label())));
+
+    // Disable the filter_test_restrict_tags_and_attributes filter plugin but
+    // have custom configuration so that the filter plugin is still configured
+    // in filtered_html the filter format.
+    $filter_config = [
+      'weight' => 20,
+      'status' => 0,
+    ];
+    $filter_format->setFilterConfig('filter_test_restrict_tags_and_attributes', $filter_config)->save();
+    // Use the get method to match the assert after the module has been
+    // uninstalled.
+    $filters = $filter_format->get('filters');
+    $this->assertTrue(isset($filters['filter_test_restrict_tags_and_attributes']), 'The filter plugin filter_test_restrict_tags_and_attributes is configured by the filtered_html filter format.');
+
+    drupal_static_reset('filter_formats');
+    \Drupal::entityManager()->getStorage('filter_format')->resetCache();
+    $module_data = _system_rebuild_module_data();
+    $this->assertFalse(isset($module_data['filter_test']->info['required']), 'The filter_test module is required.');
+
+    // Verify that a dependency exists on the module that provides the filter
+    // plugin since it has configuration for the disabled plugin.
     $this->assertEqual(['module' => ['filter_test']], $filter_format->getDependencies());
 
     // Uninstall the module.
     \Drupal::moduleHandler()->uninstall(array('filter_test'));
-    \Drupal::entityManager()->getStorage('filter_format')->resetCache();
 
-    // Verify the text format still exists but the dependency and filter is gone.
+    // Verify the filter format still exists but the dependency and filter is
+    // gone.
+    \Drupal::entityManager()->getStorage('filter_format')->resetCache();
     $filter_format = \Drupal\filter\Entity\FilterFormat::load('filtered_html');
     $this->assertEqual([], $filter_format->getDependencies());
+    // Use the get method since the FilterFormat::filters() method only returns
+    // existing plugins.
+    $filters = $filter_format->get('filters');
+    $this->assertFalse(isset($filters['filter_test_restrict_tags_and_attributes']), 'The filter plugin filter_test_restrict_tags_and_attributes is not configured by the filtered_html filter format.');
   }
 
 }
only in patch2:
unchanged:
--- a/core/modules/filter/filter.module
+++ b/core/modules/filter/filter.module
@@ -10,6 +10,7 @@
 use Drupal\Component\Utility\String;
 use Drupal\Component\Utility\Xss;
 use Drupal\Core\Cache\Cache;
+use Drupal\Core\Extension\Extension;
 use Drupal\Core\Render\Element;
 use Drupal\Core\Routing\RouteMatchInterface;
 use Drupal\Core\Session\AccountInterface;
@@ -83,6 +84,38 @@ function filter_theme() {
 }
 
 /**
+ * Implements hook_system_info_alter().
+ *
+ * Prevents uninstallation of modules that provide filter plugins that are being
+ * used in a filter format.
+ */
+function filter_system_info_alter(&$info, Extension $file, $type) {
+  // It is not safe to call filter_formats() during maintenance mode.
+  if ($type == 'module' && !defined('MAINTENANCE_MODE')) {
+    // Get filter plugins supplied by this module.
+    $filter_plugins = array_filter(\Drupal::service('plugin.manager.filter')->getDefinitions(), function ($definition) use ($file) {
+      return $definition['provider'] == $file->getName();
+    });
+    if (!empty($filter_plugins)) {
+      $used_in = [];
+      // Find out if any filter formats have the plugin enabled.
+      foreach(filter_formats() as $filter_format) {
+        foreach($filter_plugins as $filter_plugin) {
+          if ($filter_format->filters($filter_plugin['id'])->status) {
+            $used_in[] = $filter_format->label();
+            $info['required'] = TRUE;
+            break;
+          }
+        }
+      }
+      if (!empty($used_in)) {
+        $info['explanation'] = t('Provides a filter plugin that is in use in the following filter formats: %formats', array('%formats' => implode(', ', $used_in)));
+      }
+    }
+  }
+}
+
+/**
  * Retrieves a list of enabled text formats, ordered by weight.
  *
  * @param \Drupal\Core\Session\AccountInterface|null $account