diff --git a/src/modules/mavlink/mavlink_main.cpp b/src/modules/mavlink/mavlink_main.cpp
index 319c315a53..067e386579 100644
--- a/src/modules/mavlink/mavlink_main.cpp
+++ b/src/modules/mavlink/mavlink_main.cpp
@@ -147,6 +147,10 @@ Mavlink::~Mavlink()
 		} while (_task_running);
 	}
 
+	if (_instance_id >= 0) {
+		mavlink_module_instances[_instance_id] = nullptr;
+	}
+
 	perf_free(_loop_perf);
 	perf_free(_loop_interval_perf);
 	perf_free(_send_byte_error_perf);
@@ -2546,6 +2550,8 @@ Mavlink::task_main(int argc, char *argv[])
 
 	pthread_mutex_destroy(&_send_mutex);
 
+	_task_running = false;
+
 	PX4_INFO("exiting channel %i", (int)_channel);
 
 	return OK;
diff --git a/src/modules/mavlink/mavlink_main.h b/src/modules/mavlink/mavlink_main.h
index 441e2f06e3..2cc5961571 100644
--- a/src/modules/mavlink/mavlink_main.h
+++ b/src/modules/mavlink/mavlink_main.h
@@ -529,7 +529,7 @@ public:
 
 private:
 	MavlinkReceiver 	_receiver;
-	int			_instance_id{0};
+	int			_instance_id{-1};
 
 	bool			_transmitting_enabled{true};
 	bool			_transmitting_enabled_commanded{false};