diff --git a/core/config/schema/core.data_types.schema.yml b/core/config/schema/core.data_types.schema.yml
index 41332e3..404818a 100644
--- a/core/config/schema/core.data_types.schema.yml
+++ b/core/config/schema/core.data_types.schema.yml
@@ -552,7 +552,7 @@ field.value.changed:
 
 field.storage_settings.entity_reference:
   type: mapping
-  label: 'Entity reference settings'
+  label: 'Entity reference storage settings'
   mapping:
     target_type:
       type: string
@@ -560,14 +560,14 @@ field.storage_settings.entity_reference:
 
 field.field_settings.entity_reference:
   type: mapping
-  label: 'Entity reference settings'
+  label: 'Entity reference field settings'
   mapping:
     handler:
       type: string
       label: 'Reference method'
     handler_settings:
-      type: entity_reference.[%parent.handler].handler_settings
-      label: 'Reference method settings'
+      type: entity_reference_selection.[plugin_id]
+      label: 'Entity reference selection settings'
 
 field.value.entity_reference:
   type: mapping
@@ -754,3 +754,35 @@ text_format:
       label: 'Text format'
       # The text format should not be translated as part of the string
       # translation system, so this is not marked as translatable.
+
+# Schema for the configuration of the Entity reference selection plugins.
+
+entity_reference_selection:
+  type: mapping
+  label: 'Entity reference selection plugin configuration'
+  mapping:
+    plugin_id:
+      type: string
+      label: 'Entity reference selection plugin ID'
+    target_bundles:
+      type: sequence
+      label: 'types'
+      sequence:
+        - type: string
+          label: 'Type'
+    sort:
+      type: mapping
+      label: 'Sort settings'
+      mapping:
+        field:
+          type: string
+          label: 'Sort by'
+        direction:
+          type: string
+          label: 'Sort direction'
+    auto_create:
+      type: boolean
+      label: 'Create referenced entities if they don''t already exist'
+
+entity_reference_selection.*:
+  type: entity_reference_selection
diff --git a/core/lib/Drupal/Core/Entity/EntityReferenceSelection/SelectionPluginManager.php b/core/lib/Drupal/Core/Entity/EntityReferenceSelection/SelectionPluginManager.php
index 089dee8..5aadd3d 100644
--- a/core/lib/Drupal/Core/Entity/EntityReferenceSelection/SelectionPluginManager.php
+++ b/core/lib/Drupal/Core/Entity/EntityReferenceSelection/SelectionPluginManager.php
@@ -49,15 +49,22 @@ public function getInstance(array $options) {
       'handler_settings' => array(),
     );
 
+    return $this->createInstance($this->getPluginId($options['target_type'], $options['handler']), $options);
+  }
+
+  /**
+   * {@inheritdoc}
+   */
+  public function getPluginId($target_type, $base_plugin_id) {
     // Get all available selection plugins for this entity type.
-    $selection_handler_groups = $this->getSelectionGroups($options['target_type']);
+    $selection_handler_groups = $this->getSelectionGroups($target_type);
 
     // Sort the selection plugins by weight and select the best match.
-    uasort($selection_handler_groups[$options['handler']], array('Drupal\Component\Utility\SortArray', 'sortByWeightElement'));
-    end($selection_handler_groups[$options['handler']]);
-    $plugin_id = key($selection_handler_groups[$options['handler']]);
+    uasort($selection_handler_groups[$base_plugin_id], array('Drupal\Component\Utility\SortArray', 'sortByWeightElement'));
+    end($selection_handler_groups[$base_plugin_id]);
+    $plugin_id = key($selection_handler_groups[$base_plugin_id]);
 
-    return $this->createInstance($plugin_id, $options);
+    return $plugin_id;
   }
 
   /**
diff --git a/core/lib/Drupal/Core/Entity/EntityReferenceSelection/SelectionPluginManagerInterface.php b/core/lib/Drupal/Core/Entity/EntityReferenceSelection/SelectionPluginManagerInterface.php
index 81d555d..278e3c4 100644
--- a/core/lib/Drupal/Core/Entity/EntityReferenceSelection/SelectionPluginManagerInterface.php
+++ b/core/lib/Drupal/Core/Entity/EntityReferenceSelection/SelectionPluginManagerInterface.php
@@ -17,6 +17,19 @@
 interface SelectionPluginManagerInterface extends PluginManagerInterface {
 
   /**
+   * Gets the plugin ID for a given target entity type and base plugin ID.
+   *
+   * @param string $target_type
+   *   The target entity type.
+   * @param string $base_plugin_id
+   *   The base plugin ID (e.g. 'default' or 'views').
+   *
+   * @return string
+   *   The plugin ID.
+   */
+  public function getPluginId($target_type, $base_plugin_id);
+
+  /**
    * Returns selection plugins that can reference a specific entity type.
    *
    * @param string $entity_type_id
diff --git a/core/lib/Drupal/Core/Field/FieldConfigStorageBase.php b/core/lib/Drupal/Core/Field/FieldConfigStorageBase.php
index 9fb25b4..67652e5 100644
--- a/core/lib/Drupal/Core/Field/FieldConfigStorageBase.php
+++ b/core/lib/Drupal/Core/Field/FieldConfigStorageBase.php
@@ -39,7 +39,7 @@ protected function mapFromStorageRecords(array $records) {
   protected function mapToStorageRecord(EntityInterface $entity) {
     $record = parent::mapToStorageRecord($entity);
     $class = $this->fieldTypeManager->getPluginClass($record['field_type']);
-    $record['settings'] = $class::fieldSettingsToConfigData($record['settings']);
+    $record['settings'] = $class::fieldSettingsToConfigData($record['settings'], $entity);
     return $record;
   }
 
diff --git a/core/lib/Drupal/Core/Field/FieldItemBase.php b/core/lib/Drupal/Core/Field/FieldItemBase.php
index 1bb5486..1857b15 100644
--- a/core/lib/Drupal/Core/Field/FieldItemBase.php
+++ b/core/lib/Drupal/Core/Field/FieldItemBase.php
@@ -255,7 +255,7 @@ public static function storageSettingsFromConfigData(array $settings) {
   /**
    * {@inheritdoc}
    */
-  public static function fieldSettingsToConfigData(array $settings) {
+  public static function fieldSettingsToConfigData(array $settings, FieldConfigInterface $field_config) {
     return $settings;
   }
 
diff --git a/core/lib/Drupal/Core/Field/FieldItemInterface.php b/core/lib/Drupal/Core/Field/FieldItemInterface.php
index f74b3f7..4fdab39 100644
--- a/core/lib/Drupal/Core/Field/FieldItemInterface.php
+++ b/core/lib/Drupal/Core/Field/FieldItemInterface.php
@@ -309,6 +309,8 @@ public static function storageSettingsFromConfigData(array $settings);
    *
    * @param array $settings
    *   The field's settings in the field type's canonical representation.
+   * @param \Drupal\Core\Field\FieldConfigInterface $field_config
+   *   The field config entity that is about to be saved in configuration.
    *
    * @return array
    *   An array (either the unmodified $settings or a modified representation)
@@ -316,7 +318,7 @@ public static function storageSettingsFromConfigData(array $settings);
    *
    * @see \Drupal\Core\Field\FieldItemInterface::storageSettingsToConfigData()
    */
-  public static function fieldSettingsToConfigData(array $settings);
+  public static function fieldSettingsToConfigData(array $settings, FieldConfigInterface $field_config);
 
   /**
    * Returns a settings array in the field type's canonical representation.
diff --git a/core/lib/Drupal/Core/Field/Plugin/Field/FieldType/EntityReferenceItem.php b/core/lib/Drupal/Core/Field/Plugin/Field/FieldType/EntityReferenceItem.php
index 5844cf9..a1068ba 100644
--- a/core/lib/Drupal/Core/Field/Plugin/Field/FieldType/EntityReferenceItem.php
+++ b/core/lib/Drupal/Core/Field/Plugin/Field/FieldType/EntityReferenceItem.php
@@ -59,6 +59,7 @@ public static function defaultStorageSettings() {
   public static function defaultFieldSettings() {
     return array(
       'handler' => 'default',
+      'handler_settings' => array(),
     ) + parent::defaultFieldSettings();
   }
 
diff --git a/core/modules/entity_reference/config/schema/entity_reference.schema.yml b/core/modules/entity_reference/config/schema/entity_reference.schema.yml
deleted file mode 100644
index ec291fa..0000000
--- a/core/modules/entity_reference/config/schema/entity_reference.schema.yml
+++ /dev/null
@@ -1,38 +0,0 @@
-# Schema for the configuration files of the Entity Reference module.
-
-entity_reference.default.handler_settings:
-  type: mapping
-  label: 'View handler settings'
-  mapping:
-    target_bundles:
-      type: sequence
-      label: 'types'
-      sequence:
-        - type: string
-          label: 'Type'
-    sort:
-      type: mapping
-      label: 'Sort settings'
-      mapping:
-        field:
-          type: string
-          label: 'Sort by'
-        direction:
-          type: string
-          label: 'Sort direction'
-    filter:
-      type: mapping
-      label: 'Filter settings'
-      mapping:
-        type:
-          type: string
-          label: 'Filter by'
-        role:
-          type: sequence
-          label: 'Restrict to the selected roles'
-          sequence:
-            - type: string
-              label: 'Role'
-    auto_create:
-      type: boolean
-      label: 'Create referenced entities if they don''t already exist'
diff --git a/core/modules/entity_reference/entity_reference.module b/core/modules/entity_reference/entity_reference.module
index 526c60c..b4c95c2 100644
--- a/core/modules/entity_reference/entity_reference.module
+++ b/core/modules/entity_reference/entity_reference.module
@@ -84,19 +84,10 @@ function entity_reference_field_storage_config_update(FieldStorageConfigInterfac
     return;
   }
 
-  if (empty($field_storage->bundles)) {
-    // Field storage has no fields.
-    return;
-  }
-
-  $field_name = $field_storage->getName();
-
-  foreach ($field_storage->bundles() as $entity_type => $bundles) {
-    foreach ($bundles as $bundle) {
-      $field = FieldConfig::loadByName($entity_type, $bundle, $field_name);
-      $field->settings['handler_settings'] = array();
-      $field->save();
-    }
+  foreach ($field_storage->getBundles() as $bundle) {
+    $field = FieldConfig::loadByName($field_storage->getTargetEntityTypeId(), $bundle, $field_storage->getName());
+    $field->settings['handler_settings'] = array();
+    $field->save();
   }
 }
 
diff --git a/core/modules/entity_reference/src/ConfigurableEntityReferenceItem.php b/core/modules/entity_reference/src/ConfigurableEntityReferenceItem.php
index 5f0f75d..fb9898c 100644
--- a/core/modules/entity_reference/src/ConfigurableEntityReferenceItem.php
+++ b/core/modules/entity_reference/src/ConfigurableEntityReferenceItem.php
@@ -8,6 +8,7 @@
 namespace Drupal\entity_reference;
 
 use Drupal\Component\Utility\String;
+use Drupal\Core\Field\FieldConfigInterface;
 use Drupal\Core\Field\FieldStorageDefinitionInterface;
 use Drupal\Core\Field\Plugin\Field\FieldType\EntityReferenceItem;
 use Drupal\Core\Form\FormStateInterface;
@@ -45,15 +46,6 @@ public static function defaultStorageSettings() {
   /**
    * {@inheritdoc}
    */
-  public static function defaultFieldSettings() {
-    return array(
-      'handler_settings' => array(),
-    ) + parent::defaultFieldSettings();
-  }
-
-  /**
-   * {@inheritdoc}
-   */
   public function getPossibleValues(AccountInterface $account = NULL) {
     return $this->getSettableValues($account);
   }
@@ -216,4 +208,28 @@ public static function fieldSettingsFormValidate(array $form, FormStateInterface
     }
   }
 
+  /**
+   * {@inheritdoc}
+   */
+  public static function fieldSettingsToConfigData(array $settings, FieldConfigInterface $field_config) {
+    $settings = parent::fieldSettingsToConfigData($settings, $field_config);
+
+    $target_type = $field_config->getFieldStorageDefinition()->getSetting('target_type');
+    $selection_manager = \Drupal::service('plugin.manager.entity_reference_selection');
+    $settings['handler_settings']['plugin_id'] = $selection_manager->getPluginId($target_type, $settings['handler']);
+
+    return $settings;
+  }
+
+  /**
+   * {@inheritdoc}
+   */
+  public static function fieldSettingsFromConfigData(array $settings) {
+    // The 'plugin_id' handler setting is saved to config only to satisfy
+    // config schema and it is not used on runtime.
+    unset($settings['handler_settings']['plugin_id']);
+
+    return $settings;
+  }
+
 }
diff --git a/core/modules/file/config/schema/file.schema.yml b/core/modules/file/config/schema/file.schema.yml
index 70bf21f..b6195d2 100644
--- a/core/modules/file/config/schema/file.schema.yml
+++ b/core/modules/file/config/schema/file.schema.yml
@@ -46,6 +46,9 @@ base_file_field_field_settings:
     handler:
       type: string
       label: 'Reference method'
+    handler_settings:
+      type: entity_reference_selection.[plugin_id]
+      label: 'Entity reference selection settings'
     file_directory:
       type: string
       label: 'File directory'
diff --git a/core/modules/migrate_drupal/src/Tests/d6/MigrateFieldInstanceTest.php b/core/modules/migrate_drupal/src/Tests/d6/MigrateFieldInstanceTest.php
index 05cc467..daac5b2 100644
--- a/core/modules/migrate_drupal/src/Tests/d6/MigrateFieldInstanceTest.php
+++ b/core/modules/migrate_drupal/src/Tests/d6/MigrateFieldInstanceTest.php
@@ -135,11 +135,14 @@ public function testFieldInstanceSettings() {
       'display_default' => FALSE,
       'uri_scheme' => 'public',
       'handler' => 'default',
+      'handler_settings' => array(),
       'target_bundle' => NULL,
     );
+    $field_settings = $field->getSettings();
+    ksort($expected);
+    ksort($field_settings);
     // This is the only way to compare arrays.
-    $this->assertFalse(array_diff_assoc($field->getSettings(), $expected));
-    $this->assertFalse(array_diff_assoc($expected, $field->getSettings()));
+    $this->assertIdentical($expected, $field_settings);
 
     // Test a link field.
     $field = FieldConfig::load('node.story.field_test_link');
diff --git a/core/modules/taxonomy/config/schema/taxonomy.schema.yml b/core/modules/taxonomy/config/schema/taxonomy.schema.yml
index c79fa5f..f7439de 100644
--- a/core/modules/taxonomy/config/schema/taxonomy.schema.yml
+++ b/core/modules/taxonomy/config/schema/taxonomy.schema.yml
@@ -62,6 +62,9 @@ field.field_settings.taxonomy_term_reference:
     handler:
       type: string
       label: 'Reference method'
+    handler_settings:
+      type: entity_reference_selection.[plugin_id]
+      label: 'Entity reference selection settings'
 
 field.value.taxonomy_term_reference:
   type: mapping
diff --git a/core/modules/user/config/schema/user.schema.yml b/core/modules/user/config/schema/user.schema.yml
index 772deea..96101c5 100644
--- a/core/modules/user/config/schema/user.schema.yml
+++ b/core/modules/user/config/schema/user.schema.yml
@@ -174,3 +174,20 @@ condition.plugin.user_role:
       type: sequence
       sequence:
         - type: string
+
+entity_reference_selection.default:user:
+  type: entity_reference_selection
+  mapping:
+    filter:
+      type: mapping
+      label: 'Filter settings'
+      mapping:
+        type:
+          type: string
+          label: 'Filter by'
+        role:
+          type: sequence
+          label: 'Restrict to the selected roles'
+          sequence:
+            - type: string
+              label: 'Role'
diff --git a/core/modules/views/config/schema/views.entity_reference.schema.yml b/core/modules/views/config/schema/views.entity_reference.schema.yml
index 3067041..83b9dc8 100644
--- a/core/modules/views/config/schema/views.entity_reference.schema.yml
+++ b/core/modules/views/config/schema/views.entity_reference.schema.yml
@@ -1,9 +1,12 @@
 # Schema for the views entity reference selection plugins.
 
-entity_reference.views.handler_settings:
+entity_reference_selection.views:
   type: mapping
   label: 'View handler settings'
   mapping:
+    plugin_id:
+      type: string
+      label: 'Entity reference selection plugin ID'
     view:
       type: mapping
       label: 'View used to select the entities'