diff --git a/src/modules/mc_pos_control/mc_pos_control_main.cpp b/src/modules/mc_pos_control/mc_pos_control_main.cpp
index 66ffefa4a8..75b39155f9 100644
--- a/src/modules/mc_pos_control/mc_pos_control_main.cpp
+++ b/src/modules/mc_pos_control/mc_pos_control_main.cpp
@@ -268,6 +268,7 @@ private:
 
 	struct map_projection_reference_s _ref_pos;
 	float _ref_alt;
+	bool _ref_alt_is_global; /** true when the reference altitude is defined in a global reference frame */
 	hrt_abstime _ref_timestamp;
 	hrt_abstime _last_warn;
 
@@ -458,6 +459,7 @@ MulticopterPositionControl::MulticopterPositionControl() :
 	_user_intention_xy(brake),
 	_user_intention_z(brake),
 	_ref_alt(0.0f),
+	_ref_alt_is_global(false),
 	_ref_timestamp(0),
 	_last_warn(0),
 	_yaw(0.0f),
@@ -849,13 +851,15 @@ MulticopterPositionControl::update_ref()
 	// normal state when the estimator origin is set. Changing reference point in flight causes large controller
 	// setpoint changes. Changing reference point in other arming states is untested and shoud not be performed.
 	if ((_local_pos.ref_timestamp != _ref_timestamp)
-	    && (_vehicle_status.arming_state == vehicle_status_s::ARMING_STATE_STANDBY)) {
+	    && ((_vehicle_status.arming_state == vehicle_status_s::ARMING_STATE_STANDBY)
+		|| (!_ref_alt_is_global && _local_pos.z_global))) {
 		double lat_sp, lon_sp;
 		float alt_sp = 0.0f;
 
 		if (_ref_timestamp != 0) {
 			// calculate current position setpoint in global frame
 			map_projection_reproject(&_ref_pos, _pos_sp(0), _pos_sp(1), &lat_sp, &lon_sp);
+
 			// the altitude setpoint is the reference altitude (Z up) plus the (Z down)
 			// NED setpoint, multiplied out to minus
 			alt_sp = _ref_alt - _pos_sp(2);
@@ -865,6 +869,10 @@ MulticopterPositionControl::update_ref()
 		map_projection_init(&_ref_pos, _local_pos.ref_lat, _local_pos.ref_lon);
 		_ref_alt = _local_pos.ref_alt;
 
+		if (_local_pos.z_global) {
+			_ref_alt_is_global = true;
+		}
+
 		if (_ref_timestamp != 0) {
 			// reproject position setpoint to new reference
 			// this effectively adjusts the position setpoint to keep the vehicle