diff --git a/.htaccess b/.htaccess
index 05d142348b..f656d6de44 100644
--- a/.htaccess
+++ b/.htaccess
@@ -1,4 +1,3 @@
-# Version: 9.0.0
 <IfModule mod_headers.c>
   <IfModule mod_fcgid.c>
     <IfModule mod_setenvif.c>
diff --git a/lib/private/setup.php b/lib/private/setup.php
index 869a87fbf1..4d11cb44a8 100644
--- a/lib/private/setup.php
+++ b/lib/private/setup.php
@@ -369,11 +369,9 @@ class Setup {
 			// out that this is indeed an ownCloud data directory
 			file_put_contents($config->getSystemValue('datadirectory', \OC::$SERVERROOT.'/data').'/.ocdata', '');
 
-			// Update htaccess files for apache hosts
-			if (isset($_SERVER['SERVER_SOFTWARE']) && strstr($_SERVER['SERVER_SOFTWARE'], 'Apache')) {
-				self::updateHtaccess();
-				self::protectDataDirectory();
-			}
+			// Update .htaccess files
+			Setup::updateHtaccess();
+			Setup::protectDataDirectory();
 
 			//try to write logtimezone
 			if (date_default_timezone_get()) {
@@ -394,33 +392,18 @@ class Setup {
 		return \OC::$SERVERROOT.'/.htaccess';
 	}
 
-	/**
-	 * Checks if the .htaccess contains the current version parameter
-	 *
-	 * @return bool
-	 */
-	private function isCurrentHtaccess() {
-		$version = \OC_Util::getVersion();
-		unset($version[3]);
-
-		return !strpos(
-			file_get_contents($this->pathToHtaccess()),
-			'Version: '.implode('.', $version)
-		) === false;
-	}
-
 	/**
 	 * Append the correct ErrorDocument path for Apache hosts
-	 *
-	 * @throws \OC\HintException If .htaccess does not include the current version
 	 */
 	public static function updateHtaccess() {
+		// From CLI we don't know the defined web root. Thus we can't write any
+		// directives into the .htaccess file.
+		if(\OC::$CLI) {
+			return;
+		}
 		$setupHelper = new \OC\Setup(\OC::$server->getConfig(), \OC::$server->getIniWrapper(),
 			\OC::$server->getL10N('lib'), new \OC_Defaults(), \OC::$server->getLogger(),
 			\OC::$server->getSecureRandom());
-		if(!$setupHelper->isCurrentHtaccess()) {
-			throw new \OC\HintException('.htaccess file has the wrong version. Please upload the correct version. Maybe you forgot to replace it after updating?');
-		}
 
 		$htaccessContent = file_get_contents($setupHelper->pathToHtaccess());
 		$content = '';
diff --git a/tests/lib/setup.php b/tests/lib/setup.php
index 72c8452005..bc78c14008 100644
--- a/tests/lib/setup.php
+++ b/tests/lib/setup.php
@@ -130,17 +130,4 @@ class Test_OC_Setup extends \Test\TestCase {
 			->will($this->returnValue('NotAnArray'));
 		$this->setupClass->getSupportedDatabases();
 	}
-
-	/**
-	 * This is actual more an integration test whether the version parameter in the .htaccess
-	 * was updated as well when the version has been incremented.
-	 * If it hasn't this test will fail.
-	 */
-	public function testHtaccessIsCurrent() {
-		$result = self::invokePrivate(
-			$this->setupClass,
-			'isCurrentHtaccess'
-		);
-		$this->assertTrue($result);
-	}
 }