diff --git a/pylabrobot/liquid_handling/backends/hamilton/base.py b/pylabrobot/liquid_handling/backends/hamilton/base.py
index ce93d43b9fd..73ff83be6f7 100644
--- a/pylabrobot/liquid_handling/backends/hamilton/base.py
+++ b/pylabrobot/liquid_handling/backends/hamilton/base.py
@@ -84,6 +84,7 @@ def __init__(
     self.id_ = 0
 
     self._reading_thread: Optional[threading.Thread] = None
+    self._reading_thread_stop = threading.Event()
     self._waiting_tasks: List[HamiltonTask] = []
     self._tth2tti: dict[int, int] = {}  # hash to tip type index
 
@@ -101,10 +102,19 @@ def __setattr__(self, name: str, value: Any) -> None:
   async def setup(self):
     await super().setup()
     await self.io.setup()
+    self._reading_thread_stop.clear()
+    self._reading_thread = threading.Thread(target=self._reading_thread_main, daemon=True)
+    self._reading_thread.start()
 
   async def stop(self):
+    self._reading_thread_stop.set()
+    if self._reading_thread is not None:
+      self._reading_thread.join(timeout=10)
+      self._reading_thread = None
     for task in self._waiting_tasks:
-      task.fut.set_exception(RuntimeError("Stopping HamiltonLiquidHandler."))
+      task.loop.call_soon_threadsafe(
+        task.fut.set_exception, RuntimeError("Stopping HamiltonLiquidHandler.")
+      )
     self._waiting_tasks.clear()
     self._tth2tti.clear()
     await self.io.stop()
@@ -296,16 +306,16 @@ def _start_reading(
     cmd: str,
     timeout: int,
   ) -> None:
-    """Submit a task to the reading thread. Starts reading thread if it is not already running."""
+    """Submit a task to the reading thread."""
 
     timeout_time = time.time() + timeout
     self._waiting_tasks.append(
       HamiltonTask(id_=id_, loop=loop, fut=fut, cmd=cmd, timeout_time=timeout_time)
     )
 
-    # Start reading thread if it is not already running.
-    if len(self._waiting_tasks) == 1:  # self._reading_thread is None
-      self._reading_thread = threading.Thread(target=self._reading_thread_main)
+    if self._reading_thread is None or not self._reading_thread.is_alive():
+      self._reading_thread_stop.clear()
+      self._reading_thread = threading.Thread(target=self._reading_thread_main, daemon=True)
       self._reading_thread.start()
 
   @abstractmethod
@@ -326,7 +336,7 @@ def _reading_thread_main(self) -> None:
     loop.run_until_complete(self._continuously_read())
 
   async def _continuously_read(self) -> None:
-    """Continuously read from the USB port until all tasks are completed.
+    """Continuously read from the USB port until stop is requested.
 
     Tasks are stored in the `self._waiting_tasks` list, and contain a future that will be
     completed when the task is finished. Tasks are submitted to the list using the
@@ -337,7 +347,7 @@ async def _continuously_read(self) -> None:
     list. If a task has timed out, complete the future with a `TimeoutError`.
     """
 
-    while len(self._waiting_tasks) > 0:
+    while not self._reading_thread_stop.is_set():
       for idx in range(len(self._waiting_tasks) - 1, -1, -1):  # reverse order to allow deletion
         task = self._waiting_tasks[idx]
         if time.time() > task.timeout_time:
@@ -348,6 +358,10 @@ async def _continuously_read(self) -> None:
           )
           del self._waiting_tasks[idx]
 
+      if len(self._waiting_tasks) == 0:
+        await asyncio.sleep(0.01)
+        continue
+
       try:
         resp = (await self.io.read()).decode("utf-8")
       except TimeoutError:
@@ -379,8 +393,6 @@ async def _continuously_read(self) -> None:
           del self._waiting_tasks[idx]
           break
 
-    self._reading_thread = None
-
   def _ops_to_fw_positions(
     self, ops: Sequence[PipettingOp], use_channels: List[int]
   ) -> Tuple[List[int], List[int], List[bool]]: