diff --git a/clearml_agent/commands/worker.py b/clearml_agent/commands/worker.py
index eb56ebe..98b6533 100644
--- a/clearml_agent/commands/worker.py
+++ b/clearml_agent/commands/worker.py
@@ -578,7 +578,7 @@ class TaskStopSignal(object):
         self._bash_callback = shlex.split(ENV_ABORT_CALLBACK_CMD.get())
         # make sure we are re-testing in subprocesses
         os.environ[ENV_ABORT_CALLBACK_CMD.vars[0]+"_REGISTERED"] = ENV_ABORT_CALLBACK_CMD.get()
-        os.environ.pop(ENV_ABORT_CALLBACK_CMD.vars[0], None)
+        ENV_ABORT_CALLBACK_CMD.pop()
 
         # noinspection PyBroadException
         try:
@@ -611,7 +611,21 @@ class TaskStopSignal(object):
         self._self_monitor_thread.start()
         print("INFO: bash on_abort monitor thread started")
 
-    def stop_monitor_thread(self):
+    def stop_monitor_thread(self, wait_on_abort_timeout=-1):
+        # if no on_abort callback was launched, or it's done, nothing to do
+        if not self._bash_callback_thread or not self._self_monitor_thread:
+            self._self_monitor_thread = None
+            return
+
+        # we need to wait for the on_abort callback to be done
+        if wait_on_abort_timeout and wait_on_abort_timeout < 0:
+            wait_on_abort_timeout = self._abort_callback_max_timeout
+
+        if wait_on_abort_timeout:
+            tic = time()
+            while self._bash_callback_thread and (time() - tic < wait_on_abort_timeout):
+                sleep(1)
+
         self._self_monitor_thread = None
 
     def _monitor_thread_loop(self, polling_interval_sec=10):
@@ -620,6 +634,7 @@ class TaskStopSignal(object):
             stop_reason = self.test()
             if stop_reason != TaskStopSignal.default:
                 # mark quit loop
+                self._self_monitor_thread = None
                 break
 
     def _bash_callback_launch_thread(self):
@@ -641,7 +656,10 @@ class TaskStopSignal(object):
                               task=self.task_id, runtime=runtime_properties, force=True)
         except Exception as ex:
             print("WARNING: failed updating bash callback completed: {}".format(ex))
-            return
+
+        # mark we are done
+        self._bash_callback_thread = None
+        return
 
     def test(self):
         # type: () -> TaskStopReason
@@ -3224,6 +3242,9 @@ class Worker(ServiceCommandSection):
                         os.execv(command.argv[0].as_posix(), tuple([command.argv[0].as_posix()])+command.argv[1:])
                     else:
                         exit_code = command.check_call(cwd=script_dir)
+                        # if we have an on_abort callback still running, wait for it
+                        if stop_signal:
+                            stop_signal.stop_monitor_thread()
                         exit(exit_code)
                 except subprocess.CalledProcessError as ex:
                     # non zero return code
@@ -3257,6 +3278,10 @@ class Worker(ServiceCommandSection):
             self.log_traceback(e)
             exit_code = -1
 
+        # if we have an on_abort callback still running, wait for it
+        if stop_signal:
+            stop_signal.stop_monitor_thread()
+
         # kill leftover processes
         kill_all_child_processes()
 
@@ -3266,8 +3291,6 @@ class Worker(ServiceCommandSection):
         exit_code = exit_code if exit_code != ExitStatus.interrupted else -1
 
         if not disable_monitoring:
-            if stop_signal:
-                stop_signal.stop_monitor_thread()
             # we need to change task status according to exit code
             self.handle_task_termination(current_task.id, exit_code, TaskStopReason.no_stop)
             self.stop_monitor()