diff --git a/ROMFS/px4fmu_common/init.d-posix/rcS b/ROMFS/px4fmu_common/init.d-posix/rcS
index 17f00d9e24..043b9397cc 100644
--- a/ROMFS/px4fmu_common/init.d-posix/rcS
+++ b/ROMFS/px4fmu_common/init.d-posix/rcS
@@ -80,6 +80,15 @@ then
 	set AUTOCNF no
 else
 	set AUTOCNF yes
+	param set SYS_AUTOCONFIG 1
+fi
+
+if param compare SYS_AUTOCONFIG 1
+then
+	set AUTOCNF yes
+
+	# Wipe out params except RC*, flight modes, total flight time, accel cal, gyro cal, next flight UUID
+	param reset_nostart RC* COM_FLTMODE* LND_FLIGHT_T_* TC_* CAL_ACC* CAL_GYRO* COM_FLIGHT_UUID
 fi
 
 # multi-instance setup
@@ -202,6 +211,13 @@ fi
 
 sh "$autostart_file"
 
+#
+# If autoconfig parameter was set, reset it and save parameters.
+#
+if [ $AUTOCNF = yes ]
+then
+	param set SYS_AUTOCONFIG 0
+fi
 
 dataman start
 replay tryapplyparams