diff -u b/core/modules/field/modules/field_sql_storage/lib/Drupal/field_sql_storage/Entity/Tables.php b/core/modules/field/modules/field_sql_storage/lib/Drupal/field_sql_storage/Entity/Tables.php
--- b/core/modules/field/modules/field_sql_storage/lib/Drupal/field_sql_storage/Entity/Tables.php
+++ b/core/modules/field/modules/field_sql_storage/lib/Drupal/field_sql_storage/Entity/Tables.php
@@ -61,14 +61,14 @@
   function addField($field, $type, $langcode) {
     $entity_type = $this->sqlQuery->getMetaData('entity_type');
     $age = $this->sqlQuery->getMetaData('age');
-    // This variables ensures grouping works correctly. For example:
+    // This variable ensures grouping works correctly. For example:
     // ->condition('tags', 2, '>')
     // ->condition('tags', 20, '<')
     // ->condition('node_reference.nid.entity.tags', 2)
     // The first two should use the same table but the last one needs to be a
-    // new table. So for the first two, the table array index will be '0.tags'
-    // while the third will be '1.tags'.
-    $index_prefix = 0;
+    // new table. So for the first two, the table array index will be 'tags'
+    // while the third will be 'node_reference.nid.tags'.
+    $index_prefix = '';
     $specifiers = explode('.', $field);
     $base_table = 'base_table';
     $count = count($specifiers) - 1;
@@ -77,11 +77,6 @@
     $propertyDefinitions = array();
     $entity_info = entity_get_info($entity_type);
     for ($key = 0; $key <= $count; $key ++) {
-      // This can either be the name of an entity property (non-configurable
-      // field), a field API field (a configurable field) or an indication
-      // that the next specifier will be on another entity (here it'll be
-      // called relationship field).
-      $specifier = $specifiers[$key];
       // If there is revision support and only the current revision is being
       // queried then use the revision id. Otherwise, the entity id will do.
       if (!empty($entity_info['entity_keys']['revision']) && $age == FIELD_LOAD_CURRENT) {
@@ -96,13 +91,19 @@
         $entity_id_field = $entity_info['entity_keys']['id'];
         $field_id_field = 'entity_id';
       }
-      // field_purge_batch() is passing in id:$field_id.
+      // This can either be the name of an entity property (non-configurable
+      // field), a field API field (a configurable field).
+      $specifier = $specifiers[$key];
+      // First, check for field API fields by trying to retrieve the field specified.
+      // Normally it is a field name, but field_purge_batch() is passing in 
+      // id:$field_id so check that first.
       if (substr($specifier, 0, 3) == 'id:') {
         $field = field_info_field_by_id(substr($specifier, 3));
       }
       else {
         $field = field_info_field($specifier);
       }
+      // If we managed to retrieve the field, process it.
       if ($field) {
         // Find the field column.
         $column = FALSE;
@@ -136,15 +137,18 @@
               // exception anyways so no need to do it here.
               $column = $propertyDefinitions[$relationship_specifier]['settings']['id source'];
             }
+            // Prepare the next index prefix.
+            $next_index_prefix = "$relationship_specifier.$column";
           }
         }
         else {
           // If this is the last specifier, default to value.
           $column = 'value';
         }
-        $table = $this->ensureFieldTable("$index_prefix.", $field, $type, $langcode, $base_table, $entity_id_field, $field_id_field);
+        $table = $this->ensureFieldTable($index_prefix, $field, $type, $langcode, $base_table, $entity_id_field, $field_id_field);
         $sql_column = _field_sql_storage_columnname($field['field_name'], $column);
       }
+      // This is an entity property (non-configurable field).
       else {
         // ensureEntityTable() decides whether an entity property will be
         // queried from the data table or the base table based on where it
@@ -157,7 +161,7 @@
         }
         $entity_tables[$entity_info['base_table']] = drupal_get_schema($entity_info['base_table']);
         $sql_column = $specifier;
-        $table = $this->ensureEntityTable("$index_prefix.", $specifier, $type, $langcode, $base_table, $entity_id_field, $entity_tables);
+        $table = $this->ensureEntityTable($index_prefix, $specifier, $type, $langcode, $base_table, $entity_id_field, $entity_tables);
       }
       // If there are more specifiers to come, it's a relationship.
       if ($key < $count) {
@@ -176,6 +180,7 @@
           $entity = entity_create($entity_type, $values);
           $propertyDefinitions = $entity->$specifier->getPropertyDefinitions();
           $relationship_specifier = $specifiers[$key + 1];
+          $next_index_prefix = $relationship_specifier;
         }
         // Check for a valid relationship.
         if (isset($propertyDefinitions[$relationship_specifier]['constraints']['entity type']) && isset($propertyDefinitions[$relationship_specifier]['settings']['id source'])) {
@@ -185,9 +190,9 @@
           // Add the new entity base table using the table and sql column.
           $join_condition= '%alias.' . $entity_info['entity_keys']['id'] . " = $table.$sql_column";
           $base_table = $this->sqlQuery->leftJoin($entity_info['base_table'], NULL, $join_condition);
-          $index_prefix++;
           $propertyDefinitions = array();
           $key++;
+          $index_prefix .= "$next_index_prefix.";
         }
         else {
           throw new QueryException(format_string('Invalid specifier @next.', array('@next' => $next)));
diff -u b/core/modules/system/lib/Drupal/system/Tests/Entity/EntityQueryRelationshipTest.php b/core/modules/system/lib/Drupal/system/Tests/Entity/EntityQueryRelationshipTest.php
--- b/core/modules/system/lib/Drupal/system/Tests/Entity/EntityQueryRelationshipTest.php
+++ b/core/modules/system/lib/Drupal/system/Tests/Entity/EntityQueryRelationshipTest.php
@@ -69,15 +69,15 @@
     );
   }
 
-  /**
-   * Overrides \Drupal\simpletest\WebTestBase::setUp().
-   */
   protected function setUp() {
     parent::setUp();
+    // We want a taxonomy term reference field. It needs a vocabulary, terms,
+    // a field and an instance. First, create the vocabulary.
     $vocabulary = entity_create('taxonomy_vocabulary', array(
       'machine_name' => strtolower($this->randomName()),
     ));
     $vocabulary->save();
+    // Second, create the field.
     $this->fieldName = strtolower($this->randomName());
     $field = array(
       'field_name' => $this->fieldName,
@@ -85,12 +85,14 @@
     );
     $field['settings']['allowed_values']['vocabulary'] = $vocabulary->machine_name;
     field_create_field($field);
+    // Third, create the instance.
     $instance = array(
       'entity_type' => 'entity_test',
       'field_name' => $this->fieldName,
       'bundle' => 'entity_test',
     );
     field_create_instance($instance);
+    // Create two terms and also two accounts.
     for ($i = 0; $i <= 1; $i++) {
       $term = entity_create('taxonomy_term', array(
         'name' => $this->randomName(),
@@ -100,6 +102,9 @@
       $this->terms[] = $term;
       $this->accounts[] = $this->drupalCreateUser();
     }
+    // Create three entity_test entities, the 0th entity will point to the
+    // 0th account and 0th term, the 1st and 2nd entity will point to the
+    // 1st account and 1st term.
     for ($i = 0; $i <= 2; $i++) {
       $entity = entity_create('entity_test', array());
       $entity->name->value = $this->randomName();
@@ -116,36 +121,53 @@
    * Tests querying.
    */
   public function testQuery() {
+    // This returns the 0th entity as that's only one pointing to the 0th
+    // account.
     $this->queryResults = $this->factory->get('entity_test')
       ->condition("user_id.entity.name", $this->accounts[0]->name)
       ->execute();
     $this->assertResults(array(0));
+    // This returns the 1st and 2nd entity as those point to the 1st account.
     $this->queryResults = $this->factory->get('entity_test')
       ->condition("user_id.entity.name", $this->accounts[0]->name, '<>')
       ->execute();
     $this->assertResults(array(1, 2));
+    // This returns all three entities because all of them point to an
+    // account.
     $this->queryResults = $this->factory->get('entity_test')
       ->exists("user_id.entity.name")
       ->execute();
     $this->assertResults(array(0, 1, 2));
+    // This returns no entities because all of them point to an account.
     $this->queryResults = $this->factory->get('entity_test')
       ->notExists("user_id.entity.name")
       ->execute();
     $this->assertEqual(count($this->queryResults), 0);
+    // This returns the 0th entity as that's only one pointing to the 0th
+    // term (test without specifying the field column).
     $this->queryResults = $this->factory->get('entity_test')
       ->condition("$this->fieldName.entity.name", $this->terms[0]->name)
       ->execute();
     $this->assertResults(array(0));
+    // This returns the 0th entity as that's only one pointing to the 0th
+    // term (test with specifying the column name).
     $this->queryResults = $this->factory->get('entity_test')
       ->condition("$this->fieldName.tid.entity.name", $this->terms[0]->name)
       ->execute();
     $this->assertResults(array(0));
+    // This returns the 1st and 2nd entity as those point to the 1st term.
     $this->queryResults = $this->factory->get('entity_test')
       ->condition("$this->fieldName.entity.name", $this->terms[0]->name, '<>')
       ->execute();
     $this->assertResults(array(1, 2));
   }
 
+  /**
+   * Assert the results.
+   *
+   * @param array $expected
+   *   A list of indexes in the $this->entities array.
+   */
   protected function assertResults($expected) {
     $this->assertEqual(count($this->queryResults), count($expected));
     foreach ($expected as $key) {