diff --git a/homeassistant/components/github/__init__.py b/homeassistant/components/github/__init__.py
index abc376e0337..6e83ef72f68 100644
--- a/homeassistant/components/github/__init__.py
+++ b/homeassistant/components/github/__init__.py
@@ -8,12 +8,13 @@ from aiogithubapi import GitHubAPI
 from homeassistant.config_entries import ConfigEntry
 from homeassistant.const import CONF_ACCESS_TOKEN, Platform
 from homeassistant.core import HomeAssistant
+from homeassistant.helpers import device_registry as dr
 from homeassistant.helpers.aiohttp_client import (
     SERVER_SOFTWARE,
     async_get_clientsession,
 )
 
-from .const import CONF_REPOSITORIES, DOMAIN
+from .const import CONF_REPOSITORIES, DOMAIN, LOGGER
 from .coordinator import (
     DataUpdateCoordinators,
     RepositoryCommitDataUpdateCoordinator,
@@ -64,12 +65,39 @@ async def async_setup_entry(hass: HomeAssistant, entry: ConfigEntry) -> bool:
 
         hass.data[DOMAIN][repository] = coordinators
 
+    await async_cleanup_device_registry(hass=hass, entry=entry)
+
     hass.config_entries.async_setup_platforms(entry, PLATFORMS)
     entry.async_on_unload(entry.add_update_listener(async_reload_entry))
 
     return True
 
 
+async def async_cleanup_device_registry(
+    hass: HomeAssistant,
+    entry: ConfigEntry,
+) -> None:
+    """Remove entries form device registry if we no longer track the repository."""
+    device_registry = dr.async_get(hass)
+    devices = dr.async_entries_for_config_entry(
+        registry=device_registry,
+        config_entry_id=entry.entry_id,
+    )
+    for device in devices:
+        for item in device.identifiers:
+            if DOMAIN == item[0] and item[1] not in entry.options[CONF_REPOSITORIES]:
+                LOGGER.debug(
+                    "Unlinking device %s for untracked repository %s from config entry %s",
+                    device.id,
+                    item[1],
+                    entry.entry_id,
+                )
+                device_registry.async_update_device(
+                    device.id, remove_config_entry_id=entry.entry_id
+                )
+                break
+
+
 async def async_unload_entry(hass: HomeAssistant, entry: ConfigEntry) -> bool:
     """Unload a config entry."""
     if unload_ok := await hass.config_entries.async_unload_platforms(entry, PLATFORMS):
diff --git a/tests/components/github/test_init.py b/tests/components/github/test_init.py
new file mode 100644
index 00000000000..95bad95fd4c
--- /dev/null
+++ b/tests/components/github/test_init.py
@@ -0,0 +1,31 @@
+"""Test the GitHub init file."""
+from pytest import LogCaptureFixture
+
+from homeassistant.components.github import async_cleanup_device_registry
+from homeassistant.components.github.const import DOMAIN
+from homeassistant.core import HomeAssistant
+
+from tests.common import MockConfigEntry, mock_device_registry
+
+
+async def test_device_registry_cleanup(
+    hass: HomeAssistant,
+    mock_config_entry: MockConfigEntry,
+    caplog: LogCaptureFixture,
+) -> None:
+    """Test that we remove untracked repositories from the decvice registry."""
+    registry = mock_device_registry(hass)
+
+    device = registry.async_get_or_create(
+        identifiers={(DOMAIN, "test/repository")},
+        config_entry_id=mock_config_entry.entry_id,
+    )
+
+    assert registry.async_get_device({(DOMAIN, "test/repository")}) == device
+    await async_cleanup_device_registry(hass, mock_config_entry)
+
+    assert (
+        f"Unlinking device {device.id} for untracked repository test/repository from config entry {mock_config_entry.entry_id}"
+        in caplog.text
+    )
+    assert registry.async_get_device({(DOMAIN, "test/repository")}) is None