diff -u b/src/Plugin/ConfigFilter/IgnoreFilter.php b/src/Plugin/ConfigFilter/IgnoreFilter.php
--- b/src/Plugin/ConfigFilter/IgnoreFilter.php
+++ b/src/Plugin/ConfigFilter/IgnoreFilter.php
@@ -217,25 +217,9 @@
 
     }
 
-    $source = $this->source->read($name);
-    if ($source !== FALSE) {
-      foreach ($keys as $key) {
-          $parts = explode('.', $key);
-
-          if (count($parts) == 1 && isset($source[$key])) {
-            $data[$key] = $source[$key];
-          }
-          else {
-            $value = NestedArray::getValue($source, $parts, $key_exists);
-            if ($key_exists) {
-              // Enforce the value if it existed in the active config.
-              NestedArray::setValue($data, $parts, $value, TRUE);
-            }
-            else {
-              NestedArray::unsetValue($data, $parts);
-            }
-          }
-      }
+    foreach ($keys as $key) {
+      $parts = explode('.', $key);
+      NestedArray::unsetValue($data, $parts);
     }
 
     return $data;