diff --git a/homeassistant/components/zwave_js/config_flow.py b/homeassistant/components/zwave_js/config_flow.py
index 37923c574b4..ac466223fb6 100644
--- a/homeassistant/components/zwave_js/config_flow.py
+++ b/homeassistant/components/zwave_js/config_flow.py
@@ -117,7 +117,15 @@ class ConfigFlow(config_entries.ConfigFlow, domain=DOMAIN):
             await self.async_set_unique_id(
                 version_info.home_id, raise_on_progress=False
             )
-            self._abort_if_unique_id_configured(user_input)
+            # Make sure we disable any add-on handling
+            # if the controller is reconfigured in a manual step.
+            self._abort_if_unique_id_configured(
+                updates={
+                    **user_input,
+                    CONF_USE_ADDON: False,
+                    CONF_INTEGRATION_CREATED_ADDON: False,
+                }
+            )
             self.ws_address = user_input[CONF_URL]
             return self._async_create_entry_from_vars()
 
diff --git a/tests/components/zwave_js/test_config_flow.py b/tests/components/zwave_js/test_config_flow.py
index fc97f7420cf..c6b59e07412 100644
--- a/tests/components/zwave_js/test_config_flow.py
+++ b/tests/components/zwave_js/test_config_flow.py
@@ -184,7 +184,16 @@ async def test_manual_errors(
 
 async def test_manual_already_configured(hass):
     """Test that only one unique instance is allowed."""
-    entry = MockConfigEntry(domain=DOMAIN, data={}, title=TITLE, unique_id=1234)
+    entry = MockConfigEntry(
+        domain=DOMAIN,
+        data={
+            "url": "ws://localhost:3000",
+            "use_addon": True,
+            "integration_created_addon": True,
+        },
+        title=TITLE,
+        unique_id=1234,
+    )
     entry.add_to_hass(hass)
 
     await setup.async_setup_component(hass, "persistent_notification", {})
@@ -198,12 +207,15 @@ async def test_manual_already_configured(hass):
     result = await hass.config_entries.flow.async_configure(
         result["flow_id"],
         {
-            "url": "ws://localhost:3000",
+            "url": "ws://1.1.1.1:3001",
         },
     )
 
     assert result["type"] == "abort"
     assert result["reason"] == "already_configured"
+    assert entry.data["url"] == "ws://1.1.1.1:3001"
+    assert entry.data["use_addon"] is False
+    assert entry.data["integration_created_addon"] is False
 
 
 @pytest.mark.parametrize("discovery_info", [{"config": ADDON_DISCOVERY_INFO}])