diff --git a/homeassistant/bootstrap.py b/homeassistant/bootstrap.py
index 558584d68ac..391c6ebfa45 100644
--- a/homeassistant/bootstrap.py
+++ b/homeassistant/bootstrap.py
@@ -421,6 +421,9 @@ async def async_from_config_dict(
     start = monotonic()
 
     hass.config_entries = config_entries.ConfigEntries(hass, config)
+    # Prime custom component cache early so we know if registry entries are tied
+    # to a custom integration
+    await loader.async_get_custom_components(hass)
     await async_load_base_functionality(hass)
 
     # Set up core.
diff --git a/homeassistant/loader.py b/homeassistant/loader.py
index 1ad04b085b3..542f9d4f009 100644
--- a/homeassistant/loader.py
+++ b/homeassistant/loader.py
@@ -1678,6 +1678,14 @@ def async_get_issue_tracker(
         # If we know nothing about the entity, suggest opening an issue on HA core
         return issue_tracker
 
+    if (
+        not integration
+        and (hass and integration_domain)
+        and (comps_or_future := hass.data.get(DATA_CUSTOM_COMPONENTS))
+        and not isinstance(comps_or_future, asyncio.Future)
+    ):
+        integration = comps_or_future.get(integration_domain)
+
     if not integration and (hass and integration_domain):
         with suppress(IntegrationNotLoaded):
             integration = async_get_loaded_integration(hass, integration_domain)
diff --git a/tests/test_loader.py b/tests/test_loader.py
index 07fe949f882..b2ca8cbd397 100644
--- a/tests/test_loader.py
+++ b/tests/test_loader.py
@@ -2,6 +2,7 @@
 
 import asyncio
 import os
+import pathlib
 import sys
 import threading
 from typing import Any
@@ -1110,14 +1111,18 @@ CUSTOM_ISSUE_TRACKER = "https://blablabla.com"
         # Integration domain is not currently deduced from module
         (None, "homeassistant.components.hue.sensor", CORE_ISSUE_TRACKER),
         ("hue", "homeassistant.components.mqtt.sensor", CORE_ISSUE_TRACKER_HUE),
-        # Custom integration with known issue tracker
+        # Loaded custom integration with known issue tracker
         ("bla_custom", "custom_components.bla_custom.sensor", CUSTOM_ISSUE_TRACKER),
         ("bla_custom", None, CUSTOM_ISSUE_TRACKER),
-        # Custom integration without known issue tracker
+        # Loaded custom integration without known issue tracker
         (None, "custom_components.bla.sensor", None),
         ("bla_custom_no_tracker", "custom_components.bla_custom.sensor", None),
         ("bla_custom_no_tracker", None, None),
         ("hue", "custom_components.bla.sensor", None),
+        # Unloaded custom integration with known issue tracker
+        ("bla_custom_not_loaded", None, CUSTOM_ISSUE_TRACKER),
+        # Unloaded custom integration without known issue tracker
+        ("bla_custom_not_loaded_no_tracker", None, None),
         # Integration domain has priority over module
         ("bla_custom_no_tracker", "homeassistant.components.bla_custom.sensor", None),
     ],
@@ -1135,6 +1140,32 @@ async def test_async_get_issue_tracker(
         built_in=False,
     )
     mock_integration(hass, MockModule("bla_custom_no_tracker"), built_in=False)
+
+    cust_unloaded_module = MockModule(
+        "bla_custom_not_loaded",
+        partial_manifest={"issue_tracker": CUSTOM_ISSUE_TRACKER},
+    )
+    cust_unloaded = loader.Integration(
+        hass,
+        f"{loader.PACKAGE_CUSTOM_COMPONENTS}.{cust_unloaded_module.DOMAIN}",
+        pathlib.Path(""),
+        cust_unloaded_module.mock_manifest(),
+        set(),
+    )
+
+    cust_unloaded_no_tracker_module = MockModule("bla_custom_not_loaded_no_tracker")
+    cust_unloaded_no_tracker = loader.Integration(
+        hass,
+        f"{loader.PACKAGE_CUSTOM_COMPONENTS}.{cust_unloaded_no_tracker_module.DOMAIN}",
+        pathlib.Path(""),
+        cust_unloaded_no_tracker_module.mock_manifest(),
+        set(),
+    )
+    hass.data["custom_components"] = {
+        "bla_custom_not_loaded": cust_unloaded,
+        "bla_custom_not_loaded_no_tracker": cust_unloaded_no_tracker,
+    }
+
     assert (
         loader.async_get_issue_tracker(hass, integration_domain=domain, module=module)
         == issue_tracker