diff --git a/core/lib/Drupal/Core/Entity/EntityReferenceSelection/SelectionPluginBase.php b/core/lib/Drupal/Core/Entity/EntityReferenceSelection/SelectionPluginBase.php
index dfa20f4..8635755 100644
--- a/core/lib/Drupal/Core/Entity/EntityReferenceSelection/SelectionPluginBase.php
+++ b/core/lib/Drupal/Core/Entity/EntityReferenceSelection/SelectionPluginBase.php
@@ -79,11 +79,8 @@ public function setConfiguration(array $configuration) {
     //     ...
     //   - setting_N
     // @todo Remove 'handler' and 'handler_settings' in Drupal 9.0.x.
-    if (array_key_exists('handler_settings', $this->configuration)) {
-      $this->configuration = NestedArray::mergeDeep([
-        $this->configuration,
-        $this->configuration['handler_settings']
-      ]);
+    if (array_key_exists('handler_settings', $this->configuration) && is_array($this->configuration['handler_settings'])) {
+      $this->configuration = $this->configuration['handler_settings'] + $this->configuration;
     }
     // Sync back 'handler_settings'.
     foreach ($this->configuration as $key => $value) {
diff --git a/core/lib/Drupal/Core/Entity/Plugin/EntityReferenceSelection/DefaultSelection.php b/core/lib/Drupal/Core/Entity/Plugin/EntityReferenceSelection/DefaultSelection.php
index dab9f30..f041727 100644
--- a/core/lib/Drupal/Core/Entity/Plugin/EntityReferenceSelection/DefaultSelection.php
+++ b/core/lib/Drupal/Core/Entity/Plugin/EntityReferenceSelection/DefaultSelection.php
@@ -214,7 +214,7 @@ public static function elementValidateFilter(&$element, FormStateInterface $form
    * {@inheritdoc}
    */
   public function getReferenceableEntities($match = NULL, $match_operator = 'CONTAINS', $limit = 0) {
-    $target_type = $this->configuration['target_type'];
+    $target_type = $this->getConfiguration()['target_type'];
 
     $query = $this->buildEntityQuery($match, $match_operator);
     if ($limit > 0) {
diff --git a/core/modules/system/src/Tests/Entity/EntityReferenceSelection/EntityReferenceSelectionAccessTest.php b/core/modules/system/src/Tests/Entity/EntityReferenceSelection/EntityReferenceSelectionAccessTest.php
index a46fe36..b7dd8c0 100644
--- a/core/modules/system/src/Tests/Entity/EntityReferenceSelection/EntityReferenceSelectionAccessTest.php
+++ b/core/modules/system/src/Tests/Entity/EntityReferenceSelection/EntityReferenceSelectionAccessTest.php
@@ -316,7 +316,11 @@ public function testUserHandler() {
     );
     $this->assertReferenceable($selection_options, $referenceable_tests, 'User handler (admin)');
 
-    // Test the 'include_anonymous' option.
+    // Test the 'include_anonymous' option. This option is intentionally passed
+    // in the backward compatibility 'handler_settings' key to test also that
+    // plugin options passed in this way take precedence over the others, in the
+    // root. In this case the value of FALSE will override the initial value of
+    // 'include_anonymous' even that was declared in root of configuration.
     $selection_options['handler_settings']['include_anonymous'] = FALSE;
     $referenceable_tests = array(
       array(