diff --git a/changelog.d/6426.bugfix b/changelog.d/6426.bugfix
new file mode 100644
index 0000000000..3acfde4211
--- /dev/null
+++ b/changelog.d/6426.bugfix
@@ -0,0 +1 @@
+Clean up local threepids from user on account deactivation.
\ No newline at end of file
diff --git a/synapse/handlers/deactivate_account.py b/synapse/handlers/deactivate_account.py
index 63267a0a4c..6dedaaff8d 100644
--- a/synapse/handlers/deactivate_account.py
+++ b/synapse/handlers/deactivate_account.py
@@ -95,6 +95,9 @@ class DeactivateAccountHandler(BaseHandler):
                 user_id, threepid["medium"], threepid["address"]
             )
 
+        # Remove all 3PIDs this user has bound to the homeserver
+        yield self.store.user_delete_threepids(user_id)
+
         # delete any devices belonging to the user, which will also
         # delete corresponding access tokens.
         yield self._device_handler.delete_all_devices_for_user(user_id)
diff --git a/synapse/storage/data_stores/main/registration.py b/synapse/storage/data_stores/main/registration.py
index 0a3c1f0510..98cf6427c3 100644
--- a/synapse/storage/data_stores/main/registration.py
+++ b/synapse/storage/data_stores/main/registration.py
@@ -569,6 +569,19 @@ class RegistrationWorkerStore(SQLBaseStore):
         return self._simple_delete(
             "user_threepids",
             keyvalues={"user_id": user_id, "medium": medium, "address": address},
+            desc="user_delete_threepid",
+        )
+
+    def user_delete_threepids(self, user_id: str):
+        """Delete all threepid this user has bound
+
+        Args:
+             user_id: The user id to delete all threepids of
+
+        """
+        return self._simple_delete(
+            "user_threepids",
+            keyvalues={"user_id": user_id},
             desc="user_delete_threepids",
         )