diff --git a/homeassistant/components/nanoleaf/config_flow.py b/homeassistant/components/nanoleaf/config_flow.py
index 253387c254a..d62168a4ad3 100644
--- a/homeassistant/components/nanoleaf/config_flow.py
+++ b/homeassistant/components/nanoleaf/config_flow.py
@@ -10,7 +10,12 @@ from typing import Any, Final, cast
 from aionanoleaf import InvalidToken, Nanoleaf, Unauthorized, Unavailable
 import voluptuous as vol
 
-from homeassistant.config_entries import SOURCE_REAUTH, ConfigFlow, ConfigFlowResult
+from homeassistant.config_entries import (
+    SOURCE_REAUTH,
+    SOURCE_USER,
+    ConfigFlow,
+    ConfigFlowResult,
+)
 from homeassistant.const import CONF_HOST, CONF_TOKEN
 from homeassistant.helpers.aiohttp_client import async_get_clientsession
 from homeassistant.helpers.json import save_json
@@ -200,7 +205,9 @@ class NanoleafConfigFlow(ConfigFlow, domain=DOMAIN):
             return self.async_abort(reason="unknown")
         name = self.nanoleaf.name
 
-        await self.async_set_unique_id(name)
+        await self.async_set_unique_id(
+            name, raise_on_progress=self.source != SOURCE_USER
+        )
         self._abort_if_unique_id_configured({CONF_HOST: self.nanoleaf.host})
 
         if discovery_integration_import:
diff --git a/tests/components/nanoleaf/test_config_flow.py b/tests/components/nanoleaf/test_config_flow.py
index ba89405bc97..d9616572b2e 100644
--- a/tests/components/nanoleaf/test_config_flow.py
+++ b/tests/components/nanoleaf/test_config_flow.py
@@ -10,6 +10,7 @@ import pytest
 
 from homeassistant import config_entries
 from homeassistant.components.nanoleaf.const import DOMAIN
+from homeassistant.config_entries import SOURCE_USER
 from homeassistant.const import CONF_HOST, CONF_TOKEN
 from homeassistant.core import HomeAssistant
 from homeassistant.data_entry_flow import FlowResultType
@@ -463,3 +464,59 @@ async def test_ssdp_discovery(hass: HomeAssistant) -> None:
     }
 
     assert len(mock_setup_entry.mock_calls) == 1
+
+
+async def test_abort_discovery_flow_with_user_flow(hass: HomeAssistant) -> None:
+    """Test abort discovery flow if user flow is already in progress."""
+    with (
+        patch(
+            "homeassistant.components.nanoleaf.config_flow.load_json_object",
+            return_value={},
+        ),
+        patch(
+            "homeassistant.components.nanoleaf.config_flow.Nanoleaf",
+            return_value=_mock_nanoleaf(TEST_HOST, TEST_TOKEN),
+        ),
+        patch(
+            "homeassistant.components.nanoleaf.async_setup_entry",
+            return_value=True,
+        ),
+    ):
+        result = await hass.config_entries.flow.async_init(
+            DOMAIN,
+            context={"source": config_entries.SOURCE_SSDP},
+            data=SsdpServiceInfo(
+                ssdp_usn="mock_usn",
+                ssdp_st="mock_st",
+                upnp={},
+                ssdp_headers={
+                    "_host": TEST_HOST,
+                    "nl-devicename": TEST_NAME,
+                    "nl-deviceid": TEST_DEVICE_ID,
+                },
+            ),
+        )
+
+        assert result["type"] is FlowResultType.FORM
+        assert result["errors"] is None
+        assert result["step_id"] == "link"
+
+        result = await hass.config_entries.flow.async_init(
+            DOMAIN,
+            context={"source": SOURCE_USER},
+        )
+        assert len(hass.config_entries.flow.async_progress(DOMAIN)) == 2
+        assert result["type"] is FlowResultType.FORM
+        assert result["step_id"] == "user"
+
+        result = await hass.config_entries.flow.async_configure(
+            result["flow_id"], {CONF_HOST: TEST_HOST}
+        )
+        assert result["type"] is FlowResultType.FORM
+        assert result["step_id"] == "link"
+
+        result = await hass.config_entries.flow.async_configure(result["flow_id"], {})
+        assert result["type"] is FlowResultType.CREATE_ENTRY
+
+        # Verify the discovery flow was aborted
+        assert not hass.config_entries.flow.async_progress(DOMAIN)