diff --git a/synapse/handlers/presence.py b/synapse/handlers/presence.py
index 6b70fa381..2293b5fdf 100644
--- a/synapse/handlers/presence.py
+++ b/synapse/handlers/presence.py
@@ -672,7 +672,7 @@ class PresenceHandler(object):
             ])
 
     @defer.inlineCallbacks
-    def set_state(self, target_user, state):
+    def set_state(self, target_user, state, ignore_status_msg=False):
         """Set the presence state of the user.
         """
         status_msg = state.get("status_msg", None)
@@ -689,10 +689,13 @@ class PresenceHandler(object):
         prev_state = yield self.current_state_for_user(user_id)
 
         new_fields = {
-            "state": presence,
-            "status_msg": status_msg if presence != PresenceState.OFFLINE else None
+            "state": presence
         }
 
+        if not ignore_status_msg:
+            msg = status_msg if presence != PresenceState.OFFLINE else None
+            new_fields["status_msg"] = msg
+
         if presence == PresenceState.ONLINE:
             new_fields["last_active_ts"] = self.clock.time_msec()
 
diff --git a/synapse/rest/client/v2_alpha/sync.py b/synapse/rest/client/v2_alpha/sync.py
index 43d8e0bf3..b11acdbea 100644
--- a/synapse/rest/client/v2_alpha/sync.py
+++ b/synapse/rest/client/v2_alpha/sync.py
@@ -146,7 +146,7 @@ class SyncRestServlet(RestServlet):
         affect_presence = set_presence != PresenceState.OFFLINE
 
         if affect_presence:
-            yield self.presence_handler.set_state(user, {"presence": set_presence})
+            yield self.presence_handler.set_state(user, {"presence": set_presence}, True)
 
         context = yield self.presence_handler.user_syncing(
             user.to_string(), affect_presence=affect_presence,