diff --git a/ROMFS/px4fmu_common/init.d/rcS b/ROMFS/px4fmu_common/init.d/rcS
index df5c98fe0c..a304483395 100644
--- a/ROMFS/px4fmu_common/init.d/rcS
+++ b/ROMFS/px4fmu_common/init.d/rcS
@@ -798,6 +798,7 @@ then
 	if [ $VEHICLE_TYPE == passthrough ]
 	then
 		mavlink stop-all
+		commander stop
 
 		# Stop multicopter attitude controller if it is running, the controls come
 		# from Snapdragon.