diff --git a/homeassistant/config_entries.py b/homeassistant/config_entries.py
index 84771509c95..c596b71e691 100644
--- a/homeassistant/config_entries.py
+++ b/homeassistant/config_entries.py
@@ -2096,6 +2096,25 @@ class ConfigEntries:
         _setter = object.__setattr__
 
         if unique_id is not UNDEFINED and entry.unique_id != unique_id:
+            # Deprecated in 2024.11, should fail in 2025.11
+            if (
+                unique_id is not None
+                and self.async_entry_for_domain_unique_id(entry.domain, unique_id)
+                is not None
+            ):
+                report_issue = async_suggest_report_issue(
+                    self.hass, integration_domain=entry.domain
+                )
+                _LOGGER.error(
+                    (
+                        "Unique id of config entry '%s' from integration %s changed to"
+                        " '%s' which is already in use, please %s"
+                    ),
+                    entry.title,
+                    entry.domain,
+                    unique_id,
+                    report_issue,
+                )
             # Reindex the entry if the unique_id has changed
             self._entries.update_unique_id(entry, unique_id)
             changed = True
diff --git a/tests/test_config_entries.py b/tests/test_config_entries.py
index ed350f4d887..2d2ee2d936a 100644
--- a/tests/test_config_entries.py
+++ b/tests/test_config_entries.py
@@ -6788,3 +6788,31 @@ async def test_state_cache_is_cleared_on_entry_disable(hass: HomeAssistant) -> N
     )
     loaded = json_loads(json_dumps(entry.as_json_fragment))
     assert loaded["disabled_by"] == "user"
+
+
+async def test_async_update_entry_unique_id_collision(
+    hass: HomeAssistant,
+    manager: config_entries.ConfigEntries,
+    caplog: pytest.LogCaptureFixture,
+) -> None:
+    """Test we warn when async_update_entry creates a unique_id collision."""
+
+    entry1 = MockConfigEntry(domain="test", unique_id=None)
+    entry2 = MockConfigEntry(domain="test", unique_id="not none")
+    entry3 = MockConfigEntry(domain="test", unique_id="very unique")
+    entry4 = MockConfigEntry(domain="test", unique_id="also very unique")
+    entry1.add_to_manager(manager)
+    entry2.add_to_manager(manager)
+    entry3.add_to_manager(manager)
+    entry4.add_to_manager(manager)
+
+    manager.async_update_entry(entry2, unique_id=None)
+    assert len(caplog.record_tuples) == 0
+
+    manager.async_update_entry(entry4, unique_id="very unique")
+    assert len(caplog.record_tuples) == 1
+
+    assert (
+        "Unique id of config entry 'Mock Title' from integration test changed to "
+        "'very unique' which is already in use"
+    ) in caplog.text