diff --git a/ROMFS/px4fmu_common/init.d/rcS b/ROMFS/px4fmu_common/init.d/rcS
index 4a391d39f9..7d53e5b71d 100644
--- a/ROMFS/px4fmu_common/init.d/rcS
+++ b/ROMFS/px4fmu_common/init.d/rcS
@@ -93,6 +93,14 @@ then
 		fi
 	fi
 
+	# Check for an update of the ext_autostart folder, and replace the old one with it
+	if [ -e /fs/microsd/ext_autostart_new ]
+	then
+		echo "Updating external autostart files"
+		rm -r $SDCARD_EXT_PATH
+		mv /fs/microsd/ext_autostart_new $SDCARD_EXT_PATH
+	fi
+
 	set PARAM_FILE /fs/microsd/params
 	set PARAM_BACKUP_FILE "/fs/microsd/parameters_backup.bson"
 fi