diff --git a/homeassistant/helpers/device_registry.py b/homeassistant/helpers/device_registry.py
index c7f7d4c369d..463b5c4dddc 100644
--- a/homeassistant/helpers/device_registry.py
+++ b/homeassistant/helpers/device_registry.py
@@ -1460,12 +1460,18 @@ class DeviceRegistry(BaseRegistry[dict[str, list[dict[str, Any]]]]):
             if config_entry_id not in config_entries:
                 continue
             if config_entries == {config_entry_id}:
+                # Clear disabled_by if it was disabled by the config entry
+                if deleted_device.disabled_by is DeviceEntryDisabler.CONFIG_ENTRY:
+                    disabled_by = None
+                else:
+                    disabled_by = deleted_device.disabled_by
                 # Add a time stamp when the deleted device became orphaned
                 self.deleted_devices[deleted_device.id] = attr.evolve(
                     deleted_device,
                     orphaned_timestamp=now_time,
                     config_entries=set(),
                     config_entries_subentries={},
+                    disabled_by=disabled_by,
                 )
             else:
                 config_entries = config_entries - {config_entry_id}
diff --git a/homeassistant/helpers/entity_registry.py b/homeassistant/helpers/entity_registry.py
index d972b421fc4..2125c0f4512 100644
--- a/homeassistant/helpers/entity_registry.py
+++ b/homeassistant/helpers/entity_registry.py
@@ -1613,9 +1613,17 @@ class EntityRegistry(BaseRegistry):
         for key, deleted_entity in list(self.deleted_entities.items()):
             if config_entry_id != deleted_entity.config_entry_id:
                 continue
+            # Clear disabled_by if it was disabled by the config entry
+            if deleted_entity.disabled_by is RegistryEntryDisabler.CONFIG_ENTRY:
+                disabled_by = None
+            else:
+                disabled_by = deleted_entity.disabled_by
             # Add a time stamp when the deleted entity became orphaned
             self.deleted_entities[key] = attr.evolve(
-                deleted_entity, orphaned_timestamp=now_time, config_entry_id=None
+                deleted_entity,
+                orphaned_timestamp=now_time,
+                config_entry_id=None,
+                disabled_by=disabled_by,
             )
             self.async_schedule_save()
 
diff --git a/tests/helpers/test_device_registry.py b/tests/helpers/test_device_registry.py
index d056c25fc3b..d45c4f6cf91 100644
--- a/tests/helpers/test_device_registry.py
+++ b/tests/helpers/test_device_registry.py
@@ -3368,6 +3368,98 @@ async def test_cleanup_startup(hass: HomeAssistant) -> None:
     assert len(mock_call.mock_calls) == 1
 
 
+async def test_deleted_device_clears_disabled_by_on_config_entry_removal(
+    hass: HomeAssistant,
+    device_registry: dr.DeviceRegistry,
+) -> None:
+    """Test that disabled_by is cleared when config entry is removed."""
+    config_entry = MockConfigEntry(domain="test", entry_id="mock-id-1")
+    config_entry.add_to_hass(hass)
+
+    # Create a device disabled by the config entry
+    device = device_registry.async_get_or_create(
+        config_entry_id="mock-id-1",
+        identifiers={("test", "device_1")},
+        name="Test Device",
+        disabled_by=dr.DeviceEntryDisabler.CONFIG_ENTRY,
+    )
+    assert device.config_entries == {"mock-id-1"}
+    assert device.disabled_by is dr.DeviceEntryDisabler.CONFIG_ENTRY
+
+    # Remove the device (it moves to deleted_devices)
+    device_registry.async_remove_device(device.id)
+
+    assert len(device_registry.devices) == 0
+    assert len(device_registry.deleted_devices) == 1
+    deleted_device = device_registry.deleted_devices[device.id]
+    assert deleted_device.config_entries == {"mock-id-1"}
+    assert deleted_device.disabled_by is dr.DeviceEntryDisabler.CONFIG_ENTRY
+    assert deleted_device.orphaned_timestamp is None
+
+    # Clear the config entry
+    device_registry.async_clear_config_entry("mock-id-1")
+
+    # Verify disabled_by is cleared
+    deleted_device = device_registry.deleted_devices[device.id]
+    assert deleted_device.config_entries == set()
+    assert deleted_device.disabled_by is None  # Should be cleared
+    assert deleted_device.orphaned_timestamp is not None
+
+    # Now re-add the config entry and device to verify it can be enabled
+    config_entry2 = MockConfigEntry(domain="test", entry_id="mock-id-2")
+    config_entry2.add_to_hass(hass)
+
+    # Re-create the device with same identifiers
+    device2 = device_registry.async_get_or_create(
+        config_entry_id="mock-id-2",
+        identifiers={("test", "device_1")},
+        name="Test Device",
+    )
+    assert device2.config_entries == {"mock-id-2"}
+    assert device2.disabled_by is None  # Should not be disabled anymore
+    assert device2.id == device.id  # Should keep the same device id
+
+
+async def test_deleted_device_disabled_by_user_not_cleared(
+    hass: HomeAssistant,
+    device_registry: dr.DeviceRegistry,
+) -> None:
+    """Test that disabled_by=USER is not cleared when config entry is removed."""
+    config_entry = MockConfigEntry(domain="test", entry_id="mock-id-1")
+    config_entry.add_to_hass(hass)
+
+    # Create a device disabled by the user
+    device = device_registry.async_get_or_create(
+        config_entry_id="mock-id-1",
+        identifiers={("test", "device_1")},
+        name="Test Device",
+        disabled_by=dr.DeviceEntryDisabler.USER,
+    )
+    assert device.config_entries == {"mock-id-1"}
+    assert device.disabled_by is dr.DeviceEntryDisabler.USER
+
+    # Remove the device (it moves to deleted_devices)
+    device_registry.async_remove_device(device.id)
+
+    assert len(device_registry.devices) == 0
+    assert len(device_registry.deleted_devices) == 1
+    deleted_device = device_registry.deleted_devices[device.id]
+    assert deleted_device.config_entries == {"mock-id-1"}
+    assert deleted_device.disabled_by is dr.DeviceEntryDisabler.USER
+    assert deleted_device.orphaned_timestamp is None
+
+    # Clear the config entry
+    device_registry.async_clear_config_entry("mock-id-1")
+
+    # Verify disabled_by is NOT cleared for USER disabled devices
+    deleted_device = device_registry.deleted_devices[device.id]
+    assert deleted_device.config_entries == set()
+    assert (
+        deleted_device.disabled_by is dr.DeviceEntryDisabler.USER
+    )  # Should remain USER
+    assert deleted_device.orphaned_timestamp is not None
+
+
 @pytest.mark.parametrize("load_registries", [False])
 async def test_cleanup_entity_registry_change(
     hass: HomeAssistant, mock_config_entry: MockConfigEntry
diff --git a/tests/helpers/test_entity_registry.py b/tests/helpers/test_entity_registry.py
index e403333d8df..89822b80039 100644
--- a/tests/helpers/test_entity_registry.py
+++ b/tests/helpers/test_entity_registry.py
@@ -782,6 +782,97 @@ async def test_deleted_entity_removing_config_entry_id(
     assert entity_registry.deleted_entities[("light", "hue", "1234")] == deleted_entry2
 
 
+async def test_deleted_entity_clears_disabled_by_on_config_entry_removal(
+    hass: HomeAssistant,
+    entity_registry: er.EntityRegistry,
+) -> None:
+    """Test that disabled_by is cleared when config entry is removed."""
+    mock_config = MockConfigEntry(domain="light", entry_id="mock-id-1")
+    mock_config.add_to_hass(hass)
+
+    # Create an entity disabled by the config entry
+    entry = entity_registry.async_get_or_create(
+        "light",
+        "hue",
+        "5678",
+        config_entry=mock_config,
+        disabled_by=er.RegistryEntryDisabler.CONFIG_ENTRY,
+    )
+    assert entry.config_entry_id == "mock-id-1"
+    assert entry.disabled_by is er.RegistryEntryDisabler.CONFIG_ENTRY
+
+    # Remove the entity (it moves to deleted_entities)
+    entity_registry.async_remove(entry.entity_id)
+
+    assert len(entity_registry.entities) == 0
+    assert len(entity_registry.deleted_entities) == 1
+    deleted_entry = entity_registry.deleted_entities[("light", "hue", "5678")]
+    assert deleted_entry.config_entry_id == "mock-id-1"
+    assert deleted_entry.disabled_by is er.RegistryEntryDisabler.CONFIG_ENTRY
+    assert deleted_entry.orphaned_timestamp is None
+
+    # Clear the config entry
+    entity_registry.async_clear_config_entry("mock-id-1")
+
+    # Verify disabled_by is cleared
+    deleted_entry = entity_registry.deleted_entities[("light", "hue", "5678")]
+    assert deleted_entry.config_entry_id is None
+    assert deleted_entry.disabled_by is None  # Should be cleared
+    assert deleted_entry.orphaned_timestamp is not None
+
+    # Now re-add the config entry and entity to verify it can be enabled
+    mock_config2 = MockConfigEntry(domain="light", entry_id="mock-id-2")
+    mock_config2.add_to_hass(hass)
+
+    # Re-create the entity with same unique ID
+    entry2 = entity_registry.async_get_or_create(
+        "light", "hue", "5678", config_entry=mock_config2
+    )
+    assert entry2.config_entry_id == "mock-id-2"
+    assert entry2.disabled_by is None  # Should not be disabled anymore
+
+
+async def test_deleted_entity_disabled_by_user_not_cleared(
+    hass: HomeAssistant,
+    entity_registry: er.EntityRegistry,
+) -> None:
+    """Test that disabled_by=USER is not cleared when config entry is removed."""
+    mock_config = MockConfigEntry(domain="light", entry_id="mock-id-1")
+    mock_config.add_to_hass(hass)
+
+    # Create an entity disabled by the user
+    entry = entity_registry.async_get_or_create(
+        "light",
+        "hue",
+        "5678",
+        config_entry=mock_config,
+        disabled_by=er.RegistryEntryDisabler.USER,
+    )
+    assert entry.config_entry_id == "mock-id-1"
+    assert entry.disabled_by is er.RegistryEntryDisabler.USER
+
+    # Remove the entity (it moves to deleted_entities)
+    entity_registry.async_remove(entry.entity_id)
+
+    assert len(entity_registry.entities) == 0
+    assert len(entity_registry.deleted_entities) == 1
+    deleted_entry = entity_registry.deleted_entities[("light", "hue", "5678")]
+    assert deleted_entry.config_entry_id == "mock-id-1"
+    assert deleted_entry.disabled_by is er.RegistryEntryDisabler.USER
+    assert deleted_entry.orphaned_timestamp is None
+
+    # Clear the config entry
+    entity_registry.async_clear_config_entry("mock-id-1")
+
+    # Verify disabled_by is NOT cleared for USER disabled entities
+    deleted_entry = entity_registry.deleted_entities[("light", "hue", "5678")]
+    assert deleted_entry.config_entry_id is None
+    assert (
+        deleted_entry.disabled_by is er.RegistryEntryDisabler.USER
+    )  # Should remain USER
+    assert deleted_entry.orphaned_timestamp is not None
+
+
 async def test_removing_config_subentry_id(
     hass: HomeAssistant, entity_registry: er.EntityRegistry
 ) -> None: