diff --git a/framework/CHANGELOG.md b/framework/CHANGELOG.md
index e1f427477e..855850f876 100644
--- a/framework/CHANGELOG.md
+++ b/framework/CHANGELOG.md
@@ -4,6 +4,7 @@ Yii Framework 2 Change Log
 2.0.10 under development
 ------------------------
 
+- Bug #12649: Fixed consistency of `indexBy` handling for `yii\db\Query::column()` (silverfire)
 - Bug #7670: Added `UrlNormalizer` for normalizing requests with and without trailing slashes (rob006, cronfy, klimov-paul)
 - Bug #9027: Fixed descendant class of `yii\web\UploadedFile` returns parent instances in case invoked after it (andrewnester)
 - Bug #9101: Fixed `yii\web\View` to respect `yii\web\AssetManager::appendTimstamp` property (githubjeka, silverfire)
diff --git a/framework/db/Query.php b/framework/db/Query.php
index fe77784c06..2ce7656a31 100644
--- a/framework/db/Query.php
+++ b/framework/db/Query.php
@@ -268,19 +268,22 @@ class Query extends Component implements QueryInterface
      */
     public function column($db = null)
     {
-        if (!is_string($this->indexBy)) {
+        if ($this->indexBy === null) {
             return $this->createCommand($db)->queryColumn();
         }
-        if (is_array($this->select) && count($this->select) === 1) {
+
+        if (is_string($this->indexBy) && is_array($this->select) && count($this->select) === 1) {
             $this->select[] = $this->indexBy;
         }
         $rows = $this->createCommand($db)->queryAll();
         $results = [];
         foreach ($rows as $row) {
-            if (array_key_exists($this->indexBy, $row)) {
-                $results[$row[$this->indexBy]] = reset($row);
+            $value = reset($row);
+
+            if ($this->indexBy instanceof \Closure) {
+                $results[call_user_func($this->indexBy, $row)] = $value;
             } else {
-                $results[] = reset($row);
+                $results[$row[$this->indexBy]] = $value;
             }
         }
         return $results;
diff --git a/tests/framework/db/QueryTest.php b/tests/framework/db/QueryTest.php
index e21e57947a..a5a68f1420 100644
--- a/tests/framework/db/QueryTest.php
+++ b/tests/framework/db/QueryTest.php
@@ -237,6 +237,23 @@ abstract class QueryTest extends DatabaseTestCase
             ->indexBy('id')
             ->column($db);
         $this->assertEquals([3 => 'user3', 2 => 'user2', 1 => 'user1'], $result);
+
+        // https://github.com/yiisoft/yii2/issues/12649
+        $result = (new Query)->from('customer')
+            ->select(['name', 'id'])
+            ->orderBy(['id' => SORT_DESC])
+            ->indexBy(function ($row) {
+                return $row['id'] * 2;
+            })
+            ->column($db);
+        $this->assertEquals([6 => 'user3', 4 => 'user2', 2 => 'user1'], $result);
+
+        $result = (new Query)->from('customer')
+            ->select(['name'])
+            ->indexBy('name')
+            ->orderBy(['id' => SORT_DESC])
+            ->column($db);
+        $this->assertEquals(['user3' => 'user3', 'user2' => 'user2', 'user1' => 'user1'], $result);
     }
 
     public function testCount()