diff --git a/core/command/upgrade.php b/core/command/upgrade.php
index 128d27aa3dbd5c64f8df5904e8c91c6aa746cd30..6e5681b26df3a71fdce9c08b70861253783ff13c 100644
--- a/core/command/upgrade.php
+++ b/core/command/upgrade.php
@@ -27,6 +27,12 @@ class Upgrade extends Command {
 		;
 	}
 
+	/**
+	 * Execute the upgrade command
+	 *
+	 * @param InputInterface $input input interface
+	 * @param OutputInterface $output output interface
+	 */
 	protected function execute(InputInterface $input, OutputInterface $output) {
 		global $RUNTIME_NOAPPS;
 
@@ -69,6 +75,9 @@ class Upgrade extends Command {
 			});
 
 			$updater->upgrade();
+
+			$this->postUpgradeCheck($input, $output);
+
 			return self::ERROR_SUCCESS;
 		} else if(\OC_Config::getValue('maintenance', false)) {
 			//Possible scenario: ownCloud core is updated but an app failed
@@ -84,4 +93,21 @@ class Upgrade extends Command {
 			return self::ERROR_UP_TO_DATE;
 		}
 	}
+
+	/**
+	 * Perform a post upgrade check (specific to the command line tool)
+	 *
+	 * @param InputInterface $input input interface
+	 * @param OutputInterface $output output interface
+	 */
+	protected function postUpgradeCheck(InputInterface $input, OutputInterface $output) {
+		$trustedDomains = \OC_Config::getValue('trusted_domains', array());
+		if (empty($trustedDomains)) {
+			$output->write(
+				'<warning>The setting "trusted_domains" could not be ' .
+				'set automatically by the upgrade script, ' .
+				'please set it manually</warning>'
+			);
+		}
+	}
 }
diff --git a/lib/private/updater.php b/lib/private/updater.php
index fd2d46a1fac5f446a40cd864919d3929e4bf5ede..dd8dc84e80423ab302879d67eb81506f3a929cf8 100644
--- a/lib/private/updater.php
+++ b/lib/private/updater.php
@@ -108,7 +108,7 @@ class Updater extends BasicEmitter {
 		/*
 		 * START CONFIG CHANGES FOR OLDER VERSIONS
 		 */
-		if (version_compare($currentVersion, '6.90.1', '<')) {
+		if (!\OC::$CLI && version_compare($currentVersion, '6.90.1', '<')) {
 			// Add the overwriteHost config if it is not existant
 			// This is added to prevent host header poisoning
 			\OC_Config::setValue('trusted_domains', \OC_Config::getValue('trusted_domains', array(\OC_Request::serverHost())));