diff -u b/src/ConfigDiffer.php b/src/ConfigDiffer.php
--- b/src/ConfigDiffer.php
+++ b/src/ConfigDiffer.php
@@ -62,9 +62,9 @@
   /**
    * Normalizes config for comparison.
    *
-   * Removes elements in the ignore list from top level of configuration and
-   * sorts at each level by array key, so that config from different storage can
-   * be compared meaningfully.
+   * Removes elements in the ignore list from the top level of configuration,
+   * and at each level of the array, removes empty arrays and sorts by array
+   * key, so that config from different storage can be compared meaningfully.
    *
    * @param array|null $config
    *   Configuration array to normalize.
@@ -80,35 +80,39 @@
       return [];
     }
 
-    // Remove "ignore" elements.
+    // Remove "ignore" elements, only at the top level.
     foreach ($this->ignore as $element) {
       unset($config[$element]);
     }
 
-    // Recursive sort by key and return.
-    return $this->recursiveKeySort($config);
+    // Recursively normalize and return.
+    return $this->normalizeArray($config);
   }
 
   /**
-   * Recursively sort an array by key.
+   * Recursively sorts an array by key, and removes empty arrays.
    *
    * @param array $array
-   *   An array that should be sorted by keys.
+   *   An array to normalize.
    *
    * @return array
-   *   Returns a sorted array by keys.
+   *   An array that is sorted by key, at each level of the array, with empty
+   *   arrays removed.
    */
-  protected function recursiveKeySort(array $array) {
-    // Recursively normalize remaining elements, if they are arrays.
+  protected function normalizeArray(array $array) {
     foreach ($array as $key => $value) {
-      if (is_array($value) && !empty($value)) {
-        $array[$key] = $this->recursiveKeySort($value);
+      if (is_array($value)) {
+        $new = $this->normalizearray($value);
+        if (count($new)) {
+          $array[$key] = $new;
+        }
+        else {
+          unset($array[$key]);
+        }
       }
     }
 
-    // Sort and return.
     ksort($array);
-
     return $array;
   }
 
diff -u b/tests/src/Unit/ConfigDifferTest.php b/tests/src/Unit/ConfigDifferTest.php
--- b/tests/src/Unit/ConfigDifferTest.php
+++ b/tests/src/Unit/ConfigDifferTest.php
@@ -32,11 +32,10 @@
    * {@inheritdoc}
    */
   protected function setUp() {
-    // The translation is used only for formatting NULL values.
     $this->stringTranslation = $this->getMockBuilder('Drupal\Core\StringTranslation\TranslationInterface')->getMock();
     $this->stringTranslation
-      ->method('translateString')
-      ->willReturn('(NULL)');
+      ->method('t')
+      ->will($this->returnArgument(0));
 
     $this->configDiffer = new ConfigDiffer($this->stringTranslation);
   }
@@ -60,13 +59,14 @@
       'c' => [
         'd' => TRUE,
         'e' => FALSE,
+        'empty' => [],
       ],
     ];
-
     return [
       [$base, $base, TRUE],
 
-      // Add _core, omit uuid. Should match.
+      // Add _core, omit uuid at top level. Should match, as both are removed
+      // in normalization process.
       [
         $base,
         [
@@ -76,6 +76,7 @@
           'c' => [
             'd' => TRUE,
             'e' => FALSE,
+            'empty' => [],
           ],
         ],
         TRUE,
@@ -90,13 +91,15 @@
           'a' => 'a',
           'c' => [
             'e' => FALSE,
+            'empty' => [],
             'd' => TRUE,
           ],
         ],
         TRUE,
       ],
 
-      // Add _core in deeper level. Should not match.
+      // Add _core in deeper level. Should not match, as this is removed
+      // only at the top level during normalization.
       [
         $base,
         [
@@ -107,12 +110,14 @@
             '_core' => 'do-not-use-this-key',
             'd' => TRUE,
             'e' => FALSE,
+            'empty' => [],
           ],
         ],
         FALSE,
       ],
 
-      // Add uuid in deeper level. Should not match.
+      // Add uuid in deeper level. Should not match, as this is removed
+      // only at the top level during normalization.
       [
         $base,
         [
@@ -123,6 +128,7 @@
             'd' => TRUE,
             'e' => FALSE,
             'uuid' => 'important',
+            'empty' => [],
           ],
         ],
         FALSE,
@@ -137,6 +143,7 @@
           'c' => [
             'd' => TRUE,
             'e' => FALSE,
+            'empty' => [],
           ],
         ],
         FALSE,
@@ -152,6 +159,7 @@
           'c' => [
             'd' => TRUE,
             'e' => FALSE,
+            'empty' => [],
           ],
           'f' => 'f',
         ],
@@ -169,6 +177,7 @@
           'c' => [
             'd' => TRUE,
             'e' => FALSE,
+            'empty' => [],
           ],
         ],
         FALSE,
@@ -185,6 +194,7 @@
           'c' => [
             'd' => TRUE,
             'e' => FALSE,
+            'empty' => [],
           ],
         ],
         FALSE,
@@ -201,6 +211,7 @@
           'c' => [
             'd' => TRUE,
             'e' => 'e',
+            'empty' => [],
           ],
         ],
         FALSE,
@@ -217,12 +228,14 @@
           'c' => [
             'd' => 'd',
             'e' => FALSE,
+            'empty' => [],
           ],
         ],
         FALSE,
       ],
 
-      // Empty arrays should not be ignored.
+      // Add an empty array at top, and remove at lower level. Should still
+      // match.
       [
         $base,
         [
@@ -234,9 +247,9 @@
             'd' => TRUE,
             'e' => FALSE,
           ],
-          'empty_array' => [],
+          'empty_two' => [],
         ],
-        FALSE,
+        TRUE,
       ],
     ];
   }