diff --git a/homeassistant/setup.py b/homeassistant/setup.py
index 102c48e1d0741..331389da7c600 100644
--- a/homeassistant/setup.py
+++ b/homeassistant/setup.py
@@ -281,7 +281,7 @@ async def _async_setup_component(
         integration = await loader.async_get_integration(hass, domain)
     except loader.IntegrationNotFound:
         _log_error_setup_error(hass, domain, None, "Integration not found.")
-        if not hass.config.safe_mode:
+        if not hass.config.safe_mode and hass.config_entries.async_entries(domain):
             ir.async_create_issue(
                 hass,
                 HOMEASSISTANT_DOMAIN,
diff --git a/tests/components/homeassistant/test_repairs.py b/tests/components/homeassistant/test_repairs.py
index f81eaa694fac1..f84b29d8d2d8e 100644
--- a/tests/components/homeassistant/test_repairs.py
+++ b/tests/components/homeassistant/test_repairs.py
@@ -23,6 +23,7 @@ async def test_integration_not_found_confirm_step(
     await hass.async_block_till_done()
     assert await async_setup_component(hass, REPAIRS_DOMAIN, {REPAIRS_DOMAIN: {}})
     await hass.async_block_till_done()
+    MockConfigEntry(domain="test1").add_to_hass(hass)
     assert await async_setup_component(hass, "test1", {}) is False
     await hass.async_block_till_done()
     entry1 = MockConfigEntry(domain="test1")
@@ -83,6 +84,7 @@ async def test_integration_not_found_ignore_step(
     await hass.async_block_till_done()
     assert await async_setup_component(hass, REPAIRS_DOMAIN, {REPAIRS_DOMAIN: {}})
     await hass.async_block_till_done()
+    MockConfigEntry(domain="test1").add_to_hass(hass)
     assert await async_setup_component(hass, "test1", {}) is False
     await hass.async_block_till_done()
     entry1 = MockConfigEntry(domain="test1")
diff --git a/tests/test_setup.py b/tests/test_setup.py
index c50f8392d6606..2d15c670cf7bd 100644
--- a/tests/test_setup.py
+++ b/tests/test_setup.py
@@ -248,22 +248,39 @@ async def test_component_not_found(
     hass: HomeAssistant, issue_registry: IssueRegistry
 ) -> None:
     """setup_component should raise a repair issue if component doesn't exist."""
+    MockConfigEntry(domain="non_existing").add_to_hass(hass)
     assert await setup.async_setup_component(hass, "non_existing", {}) is False
     assert len(issue_registry.issues) == 1
-    issue = issue_registry.async_get_issue(
-        HOMEASSISTANT_DOMAIN, "integration_not_found.non_existing"
-    )
-    assert issue
-    assert issue.translation_key == "integration_not_found"
+    assert (
+        HOMEASSISTANT_DOMAIN,
+        "integration_not_found.non_existing",
+    ) in issue_registry.issues
+
+
+async def test_yaml_component_not_found(
+    hass: HomeAssistant, issue_registry: IssueRegistry
+) -> None:
+    """setup_component should only raise an exception for missing config entry integrations."""
+    assert await setup.async_setup_component(hass, "non_existing", {}) is False
+    assert len(issue_registry.issues) == 0
+    assert (
+        HOMEASSISTANT_DOMAIN,
+        "integration_not_found.non_existing",
+    ) not in issue_registry.issues
 
 
 async def test_component_missing_not_raising_in_safe_mode(
     hass: HomeAssistant, issue_registry: IssueRegistry
 ) -> None:
     """setup_component should not raise an issue if component doesn't exist in safe."""
+    MockConfigEntry(domain="non_existing").add_to_hass(hass)
     hass.config.safe_mode = True
     assert await setup.async_setup_component(hass, "non_existing", {}) is False
     assert len(issue_registry.issues) == 0
+    assert (
+        HOMEASSISTANT_DOMAIN,
+        "integration_not_found.non_existing",
+    ) not in issue_registry.issues
 
 
 async def test_component_not_double_initialized(hass: HomeAssistant) -> None: