diff --git a/src/Application.php b/src/Application.php
index c54da5ef30..d5ce79a167 100644
--- a/src/Application.php
+++ b/src/Application.php
@@ -351,7 +351,7 @@ protected function discoverCommandsFromConfiguration()
             }
         }
         $this->loadCommandClasses($commandList);
-        return array_keys($commandList);
+        return array_values($commandList);
     }
 
     /**
diff --git a/tests/fixtures/drush-extensions/DrushExtensionsCommands.php b/tests/fixtures/drush-extensions/DrushExtensionsCommands.php
new file mode 100644
index 0000000000..2800829b32
--- /dev/null
+++ b/tests/fixtures/drush-extensions/DrushExtensionsCommands.php
@@ -0,0 +1,20 @@
+<?php
+
+namespace Drush\Commands\drush_extensions;
+
+use Drush\Commands\DrushCommands;
+
+class DrushExtensionsCommands extends DrushCommands
+{
+    /**
+     * Command to load from this file using drush config.
+     *
+     * @command drush-extensions-hello
+     * @bootstrap none
+     * @hidden
+     */
+    public function customCommand(): void
+    {
+        $this->io()->text('Hello world!');
+    }
+}
diff --git a/tests/fixtures/drush-extensions/drush.yml b/tests/fixtures/drush-extensions/drush.yml
new file mode 100644
index 0000000000..17a3d4c09f
--- /dev/null
+++ b/tests/fixtures/drush-extensions/drush.yml
@@ -0,0 +1,8 @@
+#
+# Drush configuration file used to configure the System Unter Test (sut)
+#
+# Docs at https://github.com/drush-ops/drush/blob/master/examples/example.drush.yml
+#
+drush:
+  commands:
+    '\Drush\Commands\drush_extensions\DrushExtensionsCommands': '${env.FIXTURES_DIR}/drush-extensions/DrushExtensionsCommands.php'
\ No newline at end of file
diff --git a/tests/integration/CommandsFromConfigurationTest.php b/tests/integration/CommandsFromConfigurationTest.php
new file mode 100644
index 0000000000..021c44f8c4
--- /dev/null
+++ b/tests/integration/CommandsFromConfigurationTest.php
@@ -0,0 +1,27 @@
+<?php
+
+namespace Unish;
+
+/**
+ * @group commands
+ */
+class CommandsFromConfigurationTest extends UnishIntegrationTestCase
+{
+    /**
+     * Tests that commands provided by custom libraries are registered.
+     */
+    public function testCommandsFromConfiguration(): void
+    {
+        $this->drush('drush-extensions-hello', [], ['help' => null], self::EXIT_ERROR);
+        $this->assertStringContainsString('Command "drush-extensions-hello" is not defined.', $this->getErrorOutput());
+        $this->drush('drush-extensions-hello', [], [
+            'help' => null,
+            'config' => getenv('FIXTURES_DIR') . '/drush-extensions/drush.yml',
+        ]);
+        $this->assertStringContainsString('Command to load from this file using drush config.', $this->getOutput());
+        $this->drush('drush-extensions-hello', [], [
+            'config' => getenv('FIXTURES_DIR') . '/drush-extensions/drush.yml',
+        ]);
+        $this->assertStringContainsString('Hello world!', $this->getOutput());
+    }
+}
diff --git a/tests/unish/UnishTestCase.php b/tests/unish/UnishTestCase.php
index 2ce0861507..48d7e2d6a0 100644
--- a/tests/unish/UnishTestCase.php
+++ b/tests/unish/UnishTestCase.php
@@ -71,6 +71,7 @@ public function __construct($name = null, array $data = [], $dataName = '')
         self::setEnv(['ETC_PREFIX' => $unish_sandbox]);
         self::setEnv(['SHARE_PREFIX' => $unish_sandbox]);
         self::setEnv(['TEMP' => Path::join($unish_sandbox, 'tmp')]);
+        self::setEnv(['FIXTURES_DIR' => Path::join(dirname(__DIR__), 'fixtures')]);
     }
 
     /**