diff --git a/homeassistant/config_entries.py b/homeassistant/config_entries.py
index 5ad421755b2..aa4c7c49f99 100644
--- a/homeassistant/config_entries.py
+++ b/homeassistant/config_entries.py
@@ -1600,7 +1600,7 @@ class ConfigEntryItems(UserDict[str, ConfigEntry]):
         super().__init__()
         self._hass = hass
         self._domain_index: dict[str, list[ConfigEntry]] = {}
-        self._domain_unique_id_index: dict[str, dict[str, ConfigEntry]] = {}
+        self._domain_unique_id_index: dict[str, dict[str, list[ConfigEntry]]] = {}
 
     def values(self) -> ValuesView[ConfigEntry]:
         """Return the underlying values to avoid __iter__ overhead."""
@@ -1643,9 +1643,9 @@ class ConfigEntryItems(UserDict[str, ConfigEntry]):
                     report_issue,
                 )
 
-            self._domain_unique_id_index.setdefault(entry.domain, {})[
-                unique_id_hash
-            ] = entry
+            self._domain_unique_id_index.setdefault(entry.domain, {}).setdefault(
+                unique_id_hash, []
+            ).append(entry)
 
     def _unindex_entry(self, entry_id: str) -> None:
         """Unindex an entry."""
@@ -1658,7 +1658,9 @@ class ConfigEntryItems(UserDict[str, ConfigEntry]):
             # Check type first to avoid expensive isinstance call
             if type(unique_id) is not str and not isinstance(unique_id, Hashable):  # noqa: E721
                 unique_id = str(entry.unique_id)  # type: ignore[unreachable]
-            del self._domain_unique_id_index[domain][unique_id]
+            self._domain_unique_id_index[domain][unique_id].remove(entry)
+            if not self._domain_unique_id_index[domain][unique_id]:
+                del self._domain_unique_id_index[domain][unique_id]
             if not self._domain_unique_id_index[domain]:
                 del self._domain_unique_id_index[domain]
 
@@ -1690,7 +1692,10 @@ class ConfigEntryItems(UserDict[str, ConfigEntry]):
         # Check type first to avoid expensive isinstance call
         if type(unique_id) is not str and not isinstance(unique_id, Hashable):  # noqa: E721
             unique_id = str(unique_id)  # type: ignore[unreachable]
-        return self._domain_unique_id_index.get(domain, {}).get(unique_id)
+        entries = self._domain_unique_id_index.get(domain, {}).get(unique_id)
+        if not entries:
+            return None
+        return entries[0]
 
 
 class ConfigEntryStore(storage.Store[dict[str, list[dict[str, Any]]]]):
diff --git a/tests/test_config_entries.py b/tests/test_config_entries.py
index 3151c512e19..0ab8620057d 100644
--- a/tests/test_config_entries.py
+++ b/tests/test_config_entries.py
@@ -513,6 +513,41 @@ async def test_remove_entry(
     assert not entity_entry_list
 
 
+async def test_remove_entry_non_unique_unique_id(
+    hass: HomeAssistant,
+    manager: config_entries.ConfigEntries,
+    entity_registry: er.EntityRegistry,
+) -> None:
+    """Test that we can remove entry with colliding unique_id."""
+    entry_1 = MockConfigEntry(
+        domain="test_other", entry_id="test1", unique_id="not_unique"
+    )
+    entry_1.add_to_manager(manager)
+    entry_2 = MockConfigEntry(
+        domain="test_other", entry_id="test2", unique_id="not_unique"
+    )
+    entry_2.add_to_manager(manager)
+    entry_3 = MockConfigEntry(
+        domain="test_other", entry_id="test3", unique_id="not_unique"
+    )
+    entry_3.add_to_manager(manager)
+
+    # Check all config entries exist
+    assert manager.async_entry_ids() == [
+        "test1",
+        "test2",
+        "test3",
+    ]
+
+    # Remove entries
+    assert await manager.async_remove("test1") == {"require_restart": False}
+    await hass.async_block_till_done()
+    assert await manager.async_remove("test2") == {"require_restart": False}
+    await hass.async_block_till_done()
+    assert await manager.async_remove("test3") == {"require_restart": False}
+    await hass.async_block_till_done()
+
+
 async def test_remove_entry_cancels_reauth(
     hass: HomeAssistant,
     manager: config_entries.ConfigEntries,