diff --git a/homeassistant/components/zwave_js/config_flow.py b/homeassistant/components/zwave_js/config_flow.py
index 5519942c4441..dd855cd4a6ca 100644
--- a/homeassistant/components/zwave_js/config_flow.py
+++ b/homeassistant/components/zwave_js/config_flow.py
@@ -28,6 +28,7 @@ from homeassistant.components.hassio import (
 from homeassistant.config_entries import (
     SOURCE_ESPHOME,
     SOURCE_USB,
+    ConfigEntry,
     ConfigEntryState,
     ConfigFlow,
     ConfigFlowResult,
@@ -1516,6 +1517,7 @@ class ZWaveJSConfigFlow(ConfigFlow, domain=DOMAIN):
             return self.async_abort(reason="not_hassio")
 
         if discovery_info.zwave_home_id:
+            existing_entry: ConfigEntry | None = None
             if (
                 (
                     current_config_entries := self._async_current_entries(
@@ -1533,26 +1535,30 @@ class ZWaveJSConfigFlow(ConfigFlow, domain=DOMAIN):
                         None,
                     )
                 )
-                # Only update existing entries that are configured via sockets
-                and existing_entry.data.get(CONF_SOCKET_PATH)
-                # And use the add-on
-                and existing_entry.data.get(CONF_USE_ADDON)
             ):
-                manager = get_addon_manager(self.hass)
-                await self._async_set_addon_config(
-                    {CONF_ADDON_SOCKET: discovery_info.socket_path}
-                )
-                if self.restart_addon:
-                    await manager.async_stop_addon()
-                self.hass.config_entries.async_update_entry(
-                    existing_entry,
-                    data={
-                        **existing_entry.data,
-                        CONF_SOCKET_PATH: discovery_info.socket_path,
-                    },
-                )
-                self.hass.config_entries.async_schedule_reload(existing_entry.entry_id)
-                return self.async_abort(reason="already_configured")
+                # We can't migrate entries that are not using the add-on
+                if not existing_entry.data.get(CONF_USE_ADDON):
+                    return self.async_abort(reason="already_configured")
+
+                # Only update config automatically if using socket
+                if existing_entry.data.get(CONF_SOCKET_PATH):
+                    manager = get_addon_manager(self.hass)
+                    await self._async_set_addon_config(
+                        {CONF_ADDON_SOCKET: discovery_info.socket_path}
+                    )
+                    if self.restart_addon:
+                        await manager.async_stop_addon()
+                    self.hass.config_entries.async_update_entry(
+                        existing_entry,
+                        data={
+                            **existing_entry.data,
+                            CONF_SOCKET_PATH: discovery_info.socket_path,
+                        },
+                    )
+                    self.hass.config_entries.async_schedule_reload(
+                        existing_entry.entry_id
+                    )
+                    return self.async_abort(reason="already_configured")
 
             # We are not aborting if home ID configured here, we just want to make sure that it's set
             # We will update a USB based config entry automatically in `async_step_finish_addon_setup_user`
diff --git a/tests/components/zwave_js/test_config_flow.py b/tests/components/zwave_js/test_config_flow.py
index 40b648a3033a..71e0c963f52b 100644
--- a/tests/components/zwave_js/test_config_flow.py
+++ b/tests/components/zwave_js/test_config_flow.py
@@ -1373,7 +1373,7 @@ async def test_esphome_discovery_already_configured(
     addon_options: dict[str, Any],
     stop_addon: AsyncMock,
 ) -> None:
-    """Test ESPHome discovery success path."""
+    """Test ESPHome discovery when already configured."""
     addon_options[CONF_ADDON_SOCKET] = "esphome://existing-device:6053"
     addon_options["another_key"] = "should_not_be_touched"
 
@@ -1421,6 +1421,45 @@ async def test_esphome_discovery_already_configured(
     assert stop_addon.call_args == call("core_zwave_js")
 
 
+@pytest.mark.usefixtures("supervisor", "addon_running", "addon_info")
+async def test_esphome_discovery_already_configured_unmanaged_addon(
+    hass: HomeAssistant,
+    set_addon_options: AsyncMock,
+    addon_options: dict[str, Any],
+    stop_addon: AsyncMock,
+) -> None:
+    """Test ESPHome discovery aborts when home ID already configured with unmanaged add-on."""
+    addon_options[CONF_ADDON_SOCKET] = "esphome://existing-device:6053"
+    addon_options["another_key"] = "should_not_be_touched"
+
+    entry = MockConfigEntry(
+        entry_id="mock-entry-id",
+        domain=DOMAIN,
+        data={
+            "use_addon": False,
+            "integration_created_addon": False,
+        },
+        title=TITLE,
+        unique_id="1234",
+    )
+    entry.add_to_hass(hass)
+
+    result = await hass.config_entries.flow.async_init(
+        DOMAIN,
+        context={"source": config_entries.SOURCE_ESPHOME},
+        data=ESPHOME_DISCOVERY_INFO,
+    )
+
+    assert result["type"] is FlowResultType.ABORT
+    assert result["reason"] == "already_configured"
+
+    # Data did not get updated. Since we don't use the addon, we don't update the data
+    assert entry.data == {
+        "use_addon": False,
+        "integration_created_addon": False,
+    }
+
+
 @pytest.mark.usefixtures("supervisor", "addon_not_installed", "addon_info")
 async def test_esphome_discovery_usb_same_home_id(
     hass: HomeAssistant,