diff -u b/core/lib/Drupal/Core/Config/Config.php b/core/lib/Drupal/Core/Config/Config.php
--- b/core/lib/Drupal/Core/Config/Config.php
+++ b/core/lib/Drupal/Core/Config/Config.php
@@ -314,7 +314,15 @@
    */
   public function hasOverrides($key = '') {
     if ($key) {
-      return isset($this->moduleOverrides[$key]) || isset($this->settingsOverrides[$key]);
+      $parts = explode('.', $key);
+      $override_exists = FALSE;
+      if (isset($this->moduleOverrides) && is_array($this->moduleOverrides)) {
+        $override_exists =  NestedArray::keyExists($this->moduleOverrides, $parts);
+      }
+      if (!$override_exists && isset($this->settingsOverrides) && is_array($this->settingsOverrides)) {
+        $override_exists =  NestedArray::keyExists($this->settingsOverrides, $parts);
+      }
+      return $override_exists;
     }
     return !empty($this->moduleOverrides) || !empty($this->settingsOverrides);
   }
diff -u b/core/tests/Drupal/Tests/Core/Config/ConfigTest.php b/core/tests/Drupal/Tests/Core/Config/ConfigTest.php
--- b/core/tests/Drupal/Tests/Core/Config/ConfigTest.php
+++ b/core/tests/Drupal/Tests/Core/Config/ConfigTest.php
@@ -504,6 +504,26 @@
           'a' => 'allTheSameValue',
         ],
       ],
+      [
+        // Original data.
+        [
+          'a' => [
+            'b' => 'originalValue'
+          ],
+        ],
+        // Module overrides.
+        [
+          'a' => [
+            'b' => 'moduleValue'
+          ],
+        ],
+        // Setting overrides.
+        [
+          'a' => [
+            'b' => 'settingValue'
+          ],
+        ],
+      ],
     ];
   }
 
@@ -614,8 +634,12 @@
     }
     else {
       $this->assertTrue($this->config->hasOverrides());
-      foreach (array_keys($overridden_data) as $overridden_key) {
-        $this->assertTrue($this->config->hasOverrides($overridden_key));
+      foreach ($overridden_data as $key => $value) {
+        // If there are nested overrides test a combined key.
+        if (is_array($value)) {
+          $key = $key . '.' . key($value);
+        }
+        $this->assertTrue($this->config->hasOverrides($key));
       }
     }