diff -u b/core/lib/Drupal/Core/Entity/ContentEntityBase.php b/core/lib/Drupal/Core/Entity/ContentEntityBase.php
--- b/core/lib/Drupal/Core/Entity/ContentEntityBase.php
+++ b/core/lib/Drupal/Core/Entity/ContentEntityBase.php
@@ -158,6 +158,10 @@
   /**
    * Whether to serialize the complete entity structure.
    *
+   * Depending on the field setting "serialize_embedded_entities" of entity
+   * reference fields a deeply serialized entity might contain the referenced
+   * entities.
+   *
    * @var bool
    */
   protected $deepSerialization = FALSE;
reverted:
--- b/core/lib/Drupal/Core/Entity/ContentEntityInterface.php
+++ a/core/lib/Drupal/Core/Entity/ContentEntityInterface.php
@@ -74,23 +74,4 @@
    */
   public function updateLoadedRevisionId();
 
-  /**
-   * Returns a deeply serialized entity.
-   *
-   * @return string
-   *   The deeply serialized entity.
-   */
-  public function deepSerialize();
-
-  /**
-   * Flags the entity for deep serialization.
-   *
-   * After calling this method and serializing the entity e.g.
-   * "serialize($entity);" a deep serialization will be performed and the flag
-   * will be automatically reset.
-   *
-   * @return $this
-   */
-  public function setDeepSerialization();
-
 }
diff -u b/core/lib/Drupal/Core/Field/Plugin/Field/FieldType/EntityReferenceItem.php b/core/lib/Drupal/Core/Field/Plugin/Field/FieldType/EntityReferenceItem.php
--- b/core/lib/Drupal/Core/Field/Plugin/Field/FieldType/EntityReferenceItem.php
+++ b/core/lib/Drupal/Core/Field/Plugin/Field/FieldType/EntityReferenceItem.php
@@ -341,14 +341,6 @@
       '#element_validate' => array(array(get_class($this), 'fieldSettingsFormValidate')),
 
     );
-
-    $form['serialize_embedded_entities'] = array(
-      '#type' => 'checkbox',
-      '#title' => $this->t('Serialize entity references together with the parent entity when performing deep serialization of the parent entity.'),
-      '#description' => $this->t('If the field widget to be used for this field is an "entity reference inline widget" then the setting must be set.'),
-      '#default_value' => $field->getSetting('serialize_embedded_entities'),
-    );
-
     $form['handler'] = array(
       '#type' => 'details',
       '#title' => t('Reference type'),
diff -u b/core/modules/field/field.install b/core/modules/field/field.install
--- b/core/modules/field/field.install
+++ b/core/modules/field/field.install
@@ -115,24 +115,25 @@
  * fields.
  */
 function field_update_8300() {
-  $config = \Drupal::configFactory();
+  $config_factory = \Drupal::configFactory();
   /** @var \Drupal\Core\Field\FieldTypePluginManager $field_type_manager */
   $field_type_manager = \Drupal::service('plugin.manager.field.field_type');
 
   // Iterate over all fields.
-  foreach ($config->listAll('field.field.') as $field_id) {
-    $field = $config->getEditable($field_id);
-    $class = $field_type_manager->getPluginClass($field->get('field_type'));
+  foreach ($config_factory->listAll('field.field.') as $field_id) {
+    $field_config = $config_factory->getEditable($field_id);
+    $field_type = $field_config->get('field_type');
+    $class = $field_type_manager->getPluginClass($field_type);
 
     // Deal only with entity reference fields and descendants.
-    if ($class == EntityReferenceItem::class || is_subclass_of($class, EntityReferenceItem::class)) {
-      $settings = $field->get('settings');
+    if (($class == EntityReferenceItem::class || is_subclass_of($class, EntityReferenceItem::class)) && (strpos($field_type, 'entity_reference') === 0)) {
+      $settings = $field_config->get('settings');
 
       if (!isset($settings['serialize_embedded_entities'])) {
         $settings['serialize_embedded_entities'] = FALSE;
       }
 
-      $field->set('settings', $settings)->save(TRUE);
+      $field_config->set('settings', $settings)->save(TRUE);
     }
   }
 }
diff -u b/core/tests/Drupal/KernelTests/Core/Entity/ContentEntitySerializationTest.php b/core/tests/Drupal/KernelTests/Core/Entity/ContentEntitySerializationTest.php
--- b/core/tests/Drupal/KernelTests/Core/Entity/ContentEntitySerializationTest.php
+++ b/core/tests/Drupal/KernelTests/Core/Entity/ContentEntitySerializationTest.php
@@ -24,33 +24,33 @@
    *
    * @var string
    */
-  protected $entityTypeId;
+  protected $entityTypeId = 'entity_test_mul';
 
   /**
    * The EntityTestMul entity type storage.
    *
    * @var \Drupal\Core\Entity\ContentEntityStorageInterface
    */
-  protected $entityTestMulStorage;
+  protected $entityStorage;
+
+  /**
+   * The entity reference field name.
+   *
+   * @var string
+   */
+  protected $entityReferenceFieldName = 'field_test_entity_reference';
 
   /**
    * {@inheritdoc}
    */
   protected function setUp() {
     parent::setUp();
-    $this->entityTypeId = 'entity_test_mul';
     $this->installEntitySchema($this->entityTypeId);
-    $this->entityTestMulStorage = $this->entityManager->getStorage($this->entityTypeId);
-  }
+    $this->entityStorage = $this->entityManager->getStorage($this->entityTypeId);
 
-  /**
-   * Tests regular and deep serialization.
-   */
-  public function testSerialization() {
-    $field_name = 'field_test_entity_reference';
     // Create the test entity reference field.
     FieldStorageConfig::create([
-      'field_name' => $field_name,
+      'field_name' => $this->entityReferenceFieldName,
       'entity_type' => $this->entityTypeId,
       'type' => 'entity_reference',
       'settings' => [
@@ -63,9 +63,14 @@
       'bundle' => $this->entityTypeId,
       'translatable' => TRUE,
     ])->save();
+  }
 
-    $this->doTestSerialization(FALSE, $field_name);
-    $this->doTestSerialization(TRUE, $field_name);
+  /**
+   * Tests regular and deep serialization.
+   */
+  public function testSerialization() {
+    $this->doTestSerialization(FALSE);
+    $this->doTestSerialization(TRUE);
   }
 
   /**
@@ -73,10 +78,9 @@
    *
    * @param bool $deep_serialization
    *   Whether to test regular or deep serialization.
-   * @param bool $field_name
-   *   The name of the entity reference field.
    */
-  protected function doTestSerialization($deep_serialization, $field_name) {
+  protected function doTestSerialization($deep_serialization) {
+    $field_name = $this->entityReferenceFieldName;
     // Check that the 'target_bundle' setting contains the custom bundle.
     $field_config = FieldConfig::loadByName($this->entityTypeId, $this->entityTypeId, $field_name);
     $field_config->setSetting('serialize_embedded_entities', $deep_serialization)
@@ -87,7 +91,7 @@
 
     // Create the test entities.
     /** @var \Drupal\Core\Entity\ContentEntityInterface $entity_level_zero */
-    $entity_level_zero = $this->entityTestMulStorage->create([
+    $entity_level_zero = $this->entityStorage->create([
       'name' => $initial_entity_name,
       'user_id' => $user->id(),
       'language' => 'en',
@@ -103,14 +107,17 @@
     $entity_level_one->$field_name->appendItem($entity_level_two);
     $entity_level_one->save();
 
+    // Change the entity values in memory but do not persist them into the
+    // storage.
     $entity_level_zero->name = 'entity level zero';
     $entity_level_zero->$field_name->entity->name = 'entity level one';
     $entity_level_zero->$field_name->entity->$field_name->entity->name = 'entity level two';
 
-    $this->entityTestMulStorage->resetCache();
-
-    $serialized_entity = $entity_level_zero->deepSerialize();
+    $serialized_entity = $deep_serialization ? $entity_level_zero->deepSerialize() : serialize($entity_level_zero);
     $entity_level_zero = unserialize($serialized_entity);
+
+    // If regular serialization is tested then the changes on the referenced
+    // entities should be lost, but kept if deep serialization is tested.
     $this->assertEquals('entity level zero', $entity_level_zero->label());
     $this->assertEquals($deep_serialization ? 'entity level one' : $initial_entity_name, $entity_level_zero->$field_name->entity->label());
     $this->assertEquals($deep_serialization ? 'entity level two' : $initial_entity_name, $entity_level_zero->$field_name->entity->$field_name->entity->label());
only in patch2:
unchanged:
--- a/core/lib/Drupal/Core/Entity/FieldableEntityInterface.php
+++ b/core/lib/Drupal/Core/Entity/FieldableEntityInterface.php
@@ -236,4 +236,23 @@ public function isValidationRequired();
    */
   public function setValidationRequired($required);
 
+  /**
+   * Returns a deeply serialized entity.
+   *
+   * @return string
+   *   The deeply serialized entity.
+   */
+  public function deepSerialize();
+
+  /**
+   * Flags the entity for deep serialization.
+   *
+   * After calling this method and serializing the entity e.g.
+   * "serialize($entity);" a deep serialization will be performed and the flag
+   * will be automatically reset.
+   *
+   * @return $this
+   */
+  public function setDeepSerialization();
+
 }