diff -u b/plugins/existing_terms.inc b/plugins/existing_terms.inc
--- b/plugins/existing_terms.inc
+++ b/plugins/existing_terms.inc
@@ -84,7 +33,7 @@
 function feeds_tamper_existing_terms_callback($result, $item_key, $element_key, &$field, $settings) {
   static $allowed = array();
   if (!isset($allowed[$settings['vocabulary']])) {
-    // fetch all term names in the configured vocabulary
+    // Fetch all term names in the configured vocabulary.
     $allowed[$settings['vocabulary']] = db_query(
       'SELECT td.name 
         FROM {taxonomy_vocabulary} AS v 
@@ -95,8 +44,16 @@
     )->fetchCol('name');
   }
+  // Replace terms from the input field that are not in the allowed vocabulary
+  // with integer 0, so that they will be skipped by the taxonomy field mapping
+  // in taxonomy_feeds_set_target().
   if (is_array($field)) {
-    $field = array_intersect($field, $allowed[$settings['vocabulary']]);
-  } else {
-    $field = in_array($field, $allowed[$settings['vocabulary']]) ? $field : '';
+    foreach ($field as &$term) {
+      if (!in_array($term, $allowed[$settings['vocabulary']])) {
+        $term = 0;
+      }
+    }
+  }
+  else {
+    $field = in_array($field, $allowed[$settings['vocabulary']]) ? $field : 0;
   }
 }