diff --git a/core/Controller/SetupController.php b/core/Controller/SetupController.php
index fc1efe4c11..bb7c8c4969 100644
--- a/core/Controller/SetupController.php
+++ b/core/Controller/SetupController.php
@@ -40,7 +40,7 @@ class SetupController {
 	 * @param Setup $setupHelper
 	 */
 	function __construct(Setup $setupHelper) {
-		$this->autoConfigFile = \OC::$SERVERROOT.'/config/autoconfig.php';
+		$this->autoConfigFile = \OC::$configDir.'autoconfig.php';
 		$this->setupHelper = $setupHelper;
 	}
 
diff --git a/cron.php b/cron.php
index aac48956d1..68f6a5552d 100644
--- a/cron.php
+++ b/cron.php
@@ -90,7 +90,7 @@ try {
 			exit(0);
 		}
 		$user = posix_getpwuid(posix_getuid());
-		$configUser = posix_getpwuid(fileowner(OC::$SERVERROOT . '/config/config.php'));
+		$configUser = posix_getpwuid(fileowner(OC::$configDir . 'config.php'));
 		if ($user['name'] !== $configUser['name']) {
 			echo "Console has to be executed with the same user as the web server is operated" . PHP_EOL;
 			echo "Current user: " . $user['name'] . PHP_EOL;
diff --git a/lib/base.php b/lib/base.php
index 584f8ff502..c14452a34f 100644
--- a/lib/base.php
+++ b/lib/base.php
@@ -123,6 +123,8 @@ class OC {
 			self::$configDir = OC::$SERVERROOT . '/' . PHPUNIT_CONFIG_DIR . '/';
 		} elseif(defined('PHPUNIT_RUN') and PHPUNIT_RUN and is_dir(OC::$SERVERROOT . '/tests/config/')) {
 			self::$configDir = OC::$SERVERROOT . '/tests/config/';
+		} elseif($dir = getenv('NEXTCLOUD_CONFIG_DIR')) {
+			self::$configDir = rtrim($dir, '/') . '/';
 		} else {
 			self::$configDir = OC::$SERVERROOT . '/config/';
 		}
@@ -216,7 +218,7 @@ class OC {
 		// set the right include path
 		set_include_path(
 			OC::$SERVERROOT . '/lib/private' . PATH_SEPARATOR .
-			OC::$SERVERROOT . '/config' . PATH_SEPARATOR .
+			self::$configDir . PATH_SEPARATOR .
 			OC::$SERVERROOT . '/3rdparty' . PATH_SEPARATOR .
 			implode(PATH_SEPARATOR, $paths) . PATH_SEPARATOR .
 			get_include_path() . PATH_SEPARATOR .
diff --git a/lib/private/Server.php b/lib/private/Server.php
index 55fe71d50a..f48ce5f5c8 100644
--- a/lib/private/Server.php
+++ b/lib/private/Server.php
@@ -615,7 +615,7 @@ class Server extends ServerContainer implements IServerContainer {
 		$this->registerService('MimeTypeDetector', function (Server $c) {
 			return new \OC\Files\Type\Detection(
 				$c->getURLGenerator(),
-				\OC::$SERVERROOT . '/config/',
+				\OC::$configDir,
 				\OC::$SERVERROOT . '/resources/config/'
 			);
 		});