diff --git a/msg/vehicle_status.msg b/msg/vehicle_status.msg
index 430f7dd768..c5d5ee9a16 100644
--- a/msg/vehicle_status.msg
+++ b/msg/vehicle_status.msg
@@ -91,6 +91,7 @@ uint8 nav_state				# set navigation state machine to specified value
 uint8 arming_state			# current arming state
 uint8 hil_state				# current hil state
 bool failsafe				# true if system is in failsafe state
+bool calibration_enabled		# true if current calibrating parts of the system. Also sets the system to ARMING_STATE_INIT.
 
 int32 system_type			# system type, inspired by MAVLink's VEHICLE_TYPE enum
 int32 system_id				# system id, inspired by MAVLink's system ID field
diff --git a/src/modules/commander/commander.cpp b/src/modules/commander/commander.cpp
index 7e29dbd94d..3e9b1de6f7 100644
--- a/src/modules/commander/commander.cpp
+++ b/src/modules/commander/commander.cpp
@@ -1604,7 +1604,7 @@ int commander_thread_main(int argc, char *argv[])
 		/* End battery voltage check */
 
 		/* If in INIT state, try to proceed to STANDBY state */
-		if (status.arming_state == vehicle_status_s::ARMING_STATE_INIT) {
+		if (!status.calibration_enabled && status.arming_state == vehicle_status_s::ARMING_STATE_INIT) {
 			arming_ret = arming_state_transition(&status, &safety, vehicle_status_s::ARMING_STATE_STANDBY, &armed, true /* fRunPreArmChecks */,
 							     mavlink_fd);
 
@@ -2689,6 +2689,8 @@ void *commander_low_prio_loop(void *arg)
 							false /* fRunPreArmChecks */, mavlink_fd)) {
 						answer_command(cmd, VEHICLE_CMD_RESULT_DENIED);
 						break;
+					} else {
+						status.calibration_enabled = true;
 					}
 
 					if ((int)(cmd.param1) == 1) {
@@ -2748,12 +2750,14 @@ void *commander_low_prio_loop(void *arg)
 							/* enable RC control input */
 							status.rc_input_blocked = false;
 							mavlink_log_info(mavlink_fd, "CAL: Re-enabling RC IN");
-                            calib_ret = OK;
+							calib_ret = OK;
 						}
 						/* this always succeeds */
 						calib_ret = OK;
 					}
 
+					status.calibration_enabled = false;
+
 					if (calib_ret == OK) {
 						tune_positive(true);
 
@@ -2771,7 +2775,7 @@ void *commander_low_prio_loop(void *arg)
 
 						status.condition_system_sensors_initialized = Commander::preflightCheck(mavlink_fd, true, true, true, true, checkAirspeed, true, !status.circuit_breaker_engaged_gpsfailure_check);
 
-						arming_state_transition(&status, &safety, vehicle_status_s::ARMING_STATE_STANDBY, &armed, true /* fRunPreArmChecks */, mavlink_fd);
+						arming_state_transition(&status, &safety, vehicle_status_s::ARMING_STATE_STANDBY, &armed, false /* fRunPreArmChecks */, mavlink_fd);
 
 					} else {
 						tune_negative(true);
diff --git a/src/modules/commander/state_machine_helper.cpp b/src/modules/commander/state_machine_helper.cpp
index 2d631305dd..b53eeebeb6 100644
--- a/src/modules/commander/state_machine_helper.cpp
+++ b/src/modules/commander/state_machine_helper.cpp
@@ -216,17 +216,6 @@ arming_state_transition(struct vehicle_status_s *status,		///< current vehicle s
 			valid_transition = true;
 		}
 
-		// Sensors need to be initialized for STANDBY state, except for HIL
-		if ((status->hil_state != vehicle_status_s::HIL_STATE_ON) &&
-			(new_arming_state == vehicle_status_s::ARMING_STATE_STANDBY) &&
-			(status->arming_state != vehicle_status_s::ARMING_STATE_STANDBY_ERROR) &&
-			(!status->condition_system_sensors_initialized)) {
-			mavlink_and_console_log_critical(mavlink_fd, "Not ready to fly: Sensors need inspection");
-			feedback_provided = true;
-			valid_transition = false;
-			status->arming_state = vehicle_status_s::ARMING_STATE_STANDBY_ERROR;
-		}
-
 		// Check if we are trying to arm, checks look good but we are in STANDBY_ERROR
 		if (status->arming_state == vehicle_status_s::ARMING_STATE_STANDBY_ERROR) {
 
@@ -244,8 +233,21 @@ arming_state_transition(struct vehicle_status_s *status,		///< current vehicle s
 				mavlink_and_console_log_critical(mavlink_fd, "Preflight check resolved, reboot to complete");
 				feedback_provided = true;
 			} else {
-
+				// Silent ignore
+				feedback_provided = true;
 			}
+
+		// Sensors need to be initialized for STANDBY state, except for HIL
+		} else if ((status->hil_state != vehicle_status_s::HIL_STATE_ON) &&
+			(new_arming_state == vehicle_status_s::ARMING_STATE_STANDBY) &&
+			(status->arming_state != vehicle_status_s::ARMING_STATE_STANDBY_ERROR) &&
+			(!status->condition_system_sensors_initialized)) {
+			if (!fRunPreArmChecks) {
+				mavlink_and_console_log_critical(mavlink_fd, "Not ready to fly: Sensors need inspection");
+			}
+			feedback_provided = true;
+			valid_transition = false;
+			status->arming_state = vehicle_status_s::ARMING_STATE_STANDBY_ERROR;
 		}
 
 		// Finish up the state transition