diff --git a/core/lib/Drupal/Core/Config/ConfigFactoryOverrideBase.php b/core/lib/Drupal/Core/Config/ConfigFactoryOverrideBase.php
index 3ff2f24..b42670f 100644
--- a/core/lib/Drupal/Core/Config/ConfigFactoryOverrideBase.php
+++ b/core/lib/Drupal/Core/Config/ConfigFactoryOverrideBase.php
@@ -95,7 +95,8 @@ protected function filterNestedArray(array $original_data, array &$override_data
       elseif (is_array($override_data[$key])) {
         if (is_array($original_data[$key])) {
           // Do the filtering one level deeper.
-          $changed = $this->filterNestedArray($original_data[$key], $override_data[$key]);
+          // Ensure that we track that we changed something along the way.
+          $changed = $this->filterNestedArray($original_data[$key], $override_data[$key]) || $changed;
           // If no overrides are left under this level, remove the level.
           if (empty($override_data[$key])) {
             unset($override_data[$key]);
diff --git a/core/tests/Drupal/Tests/Core/Config/ConfigFactoryOverrideBaseTest.php b/core/tests/Drupal/Tests/Core/Config/ConfigFactoryOverrideBaseTest.php
new file mode 100644
index 0000000..4d860cd
--- /dev/null
+++ b/core/tests/Drupal/Tests/Core/Config/ConfigFactoryOverrideBaseTest.php
@@ -0,0 +1,94 @@
+<?php
+
+namespace Drupal\Tests\Core\Config;
+
+use Drupal\Core\Config\ConfigCollectionInfo;
+use Drupal\Core\Config\ConfigCrudEvent;
+use Drupal\Core\Config\ConfigFactoryOverrideBase;
+use Drupal\Core\Config\ConfigRenameEvent;
+
+/**
+ * @coversDefaultClass \Drupal\Core\Config\ConfigFactoryOverrideBase
+ * @group config
+ */
+class ConfigFactoryOverrideBaseTest extends \PHPUnit_Framework_TestCase {
+
+  /**
+   * @dataProvider providerTestFilterNestedArray
+   */
+  public function testFilterNestedArray(array $original_data, array $override_data_before, array $override_data_after, $changed) {
+    $config_factory = new TestConfigFactoryOverrideBase();
+    $result = $config_factory->doFilterNestedArray($original_data, $override_data_before);
+    $this->assertEquals($changed, $result);
+    $this->assertEquals($override_data_after, $override_data_before);
+  }
+
+  public function providerTestFilterNestedArray() {
+    $data = [];
+    $data['empty'] = [
+      [],
+      [],
+      [],
+      FALSE,
+    ];
+
+    $data['one-level-no-change'] = [
+      ['key' => 'value'],
+      [],
+      [],
+      FALSE,
+    ];
+
+    $data['one-level-override-no-change'] = [
+      ['key' => 'value'],
+      ['key' => 'value2'],
+      ['key' => 'value2'],
+      FALSE,
+    ];
+
+    $data['one-level-override-change'] = [
+      ['key' => 'value'],
+      ['key2' => 'value2'],
+      [],
+      TRUE,
+    ];
+
+    $data['one-level-multiple-override-change'] = [
+      ['key' => 'value', 'key2' => 'value2'],
+      ['key2' => 'value2', 'key3' => 'value3'],
+      ['key2' => 'value2'],
+      TRUE,
+    ];
+
+    $data['multiple-level-multiple-override-change'] = [
+      ['key' => ['key' => 'value'], 'key2' => ['key' => 'value']],
+      ['key' => ['key2' => 'value2'], 'key2' => ['key' => 'value']],
+      ['key2' => ['key' => 'value']],
+      TRUE,
+    ];
+
+    return $data;
+  }
+
+}
+
+
+class TestConfigFactoryOverrideBase extends ConfigFactoryOverrideBase {
+
+  public function doFilterNestedArray(array $original_data, array &$override_data) {
+    return $this->filterNestedArray($original_data, $override_data);
+  }
+
+  public function addCollections(ConfigCollectionInfo $collection_info) {
+  }
+
+  public function onConfigSave(ConfigCrudEvent $event) {
+  }
+
+  public function onConfigDelete(ConfigCrudEvent $event) {
+  }
+
+  public function onConfigRename(ConfigRenameEvent $event) {
+  }
+
+}