diff --git a/src/modules/mavlink/mavlink_main.cpp b/src/modules/mavlink/mavlink_main.cpp
index 9ab591f997..1b72a220b0 100644
--- a/src/modules/mavlink/mavlink_main.cpp
+++ b/src/modules/mavlink/mavlink_main.cpp
@@ -162,13 +162,6 @@ Mavlink::~Mavlink()
 		} while (running());
 	}
 
-	if (_instance_id >= 0) {
-		{
-			LockGuard lg{mavlink_module_mutex};
-			mavlink_module_instances[_instance_id] = nullptr;
-		}
-		mavlink_instance_count.fetch_sub(1);
-	}
 
 	// if this instance was responsible for checking events then select a new mavlink instance
 	if (check_events()) {
@@ -381,8 +374,13 @@ Mavlink::destroy_all_instances()
 		LockGuard lg{mavlink_module_mutex};
 
 		// we know all threads have exited, so it's safe to delete objects.
-		for (Mavlink *inst_to_del : mavlink_module_instances) {
-			delete inst_to_del;
+		for (int i = 0; i < MAVLINK_COMM_NUM_BUFFERS; i++) {
+			if (mavlink_module_instances[i] != nullptr) {
+				Mavlink *inst = mavlink_module_instances[i];
+				mavlink_module_instances[i] = nullptr;
+				mavlink_instance_count.fetch_sub(1);
+				delete inst;
+			}
 		}
 	}
 
@@ -2921,6 +2919,14 @@ int Mavlink::start_helper(int argc, char *argv[])
 		res = instance->task_main(argc, argv);
 
 		if (res != PX4_OK) {
+			LockGuard lg{mavlink_module_mutex};
+			int instance_id = instance->get_instance_id();
+
+			if (instance_id >= 0) {
+				mavlink_module_instances[instance_id] = nullptr;
+				mavlink_instance_count.fetch_sub(1);
+			}
+
 			delete instance;
 		}
 	}
@@ -3235,8 +3241,9 @@ Mavlink::stop_command(int argc, char *argv[])
 
 				for (int mavlink_instance = 0; mavlink_instance < MAVLINK_COMM_NUM_BUFFERS; mavlink_instance++) {
 					if (mavlink_module_instances[mavlink_instance] == inst) {
-						delete inst;
 						mavlink_module_instances[mavlink_instance] = nullptr;
+						mavlink_instance_count.fetch_sub(1);
+						delete inst;
 						return PX4_OK;
 					}
 				}