diff --git a/plugins/selection/EntityReference_SelectionHandler_Generic.class.php b/plugins/selection/EntityReference_SelectionHandler_Generic.class.php
index 35f06f5..c0562e2 100644
--- a/plugins/selection/EntityReference_SelectionHandler_Generic.class.php
+++ b/plugins/selection/EntityReference_SelectionHandler_Generic.class.php
@@ -306,6 +306,50 @@ class EntityReference_SelectionHandler_Generic implements EntityReference_Select
   public function getLabel($entity) {
     return entity_label($this->field['settings']['target_type'], $entity);
   }
+
+  /**
+   * Ensure a base table exists for the query.
+   *
+   * If we have a field-only query, we want to assure we have a base-table
+   * so we can later alter the query in entityFieldQueryAlter().
+   *
+   * @param $query
+   *   The Select query.
+   *
+   * @return
+   *   The alias of the base-table.
+   */
+  public function ensureBaseTable(SelectQueryInterface $query) {
+    $tables = $query->getTables();
+
+    // Check the current base table.
+    foreach ($tables as $table) {
+      if (empty($table['join'])) {
+        $alias = $table['alias'];
+      }
+    }
+
+    if (strpos($alias, 'field_data_') !== 0) {
+      // The existing base-table is the correct one.
+      return $alias;
+    }
+
+    // Iterate over the conditions, until we find the expected entity-type.
+    $conditions = $query->conditions();
+    foreach ($conditions as $key => $condition) {
+      if (!is_numeric($key)) {
+        continue;
+      }
+
+      if ($condition['field'] == "$alias.entity_type") {
+        $base_table = $condition['value'];
+        $entity_info = entity_get_info($base_table);
+        $id = $entity_info['entity keys']['id'];
+        // Return the alias of the table.
+        return $query->innerJoin($base_table, NULL, "$base_table.$id = $alias.entity_id");
+      }
+    }
+  }
 }
 
 /**
@@ -321,8 +365,8 @@ class EntityReference_SelectionHandler_Generic_node extends EntityReference_Sele
     // modules in use on the site. As long as one access control module is there,
     // it is supposed to handle this check.
     if (!user_access('bypass node access') && !count(module_implements('node_grants'))) {
-      $tables = $query->getTables();
-      $query->condition(key($tables) . '.status', NODE_PUBLISHED);
+      $base_table = $this->ensureBaseTable($query);
+      $query->condition("$base_table.status", NODE_PUBLISHED);
     }
   }
 }
@@ -396,8 +440,8 @@ class EntityReference_SelectionHandler_Generic_comment extends EntityReference_S
     // requires us to also know about the concept of 'published' and
     // 'unpublished'.
     if (!user_access('administer comments')) {
-      $tables = $query->getTables();
-      $query->condition(key($tables) . '.status', COMMENT_PUBLISHED);
+      $base_table = $this->ensureBaseTable($query);
+      $query->condition("$base_table.status", COMMENT_PUBLISHED);
     }
 
     // The Comment module doesn't implement any proper comment access,
@@ -469,8 +513,7 @@ class EntityReference_SelectionHandler_Generic_taxonomy_term extends EntityRefer
     // The Taxonomy module doesn't implement any proper taxonomy term access,
     // and as a consequence doesn't make sure that taxonomy terms cannot be viewed
     // when the user doesn't have access to the vocabulary.
-    $tables = $query->getTables();
-    $base_table = key($tables);
+    $base_table = $this->ensureBaseTable($query);
     $vocabulary_alias = $query->innerJoin('taxonomy_vocabulary', 'n', '%alias.vid = ' . $base_table . '.vid');
     $query->addMetadata('base_table', $vocabulary_alias);
     // Pass the query to the taxonomy access control.