diff --git a/homeassistant/config_entries.py b/homeassistant/config_entries.py
index ec0a559c76f..f9e72a723a4 100644
--- a/homeassistant/config_entries.py
+++ b/homeassistant/config_entries.py
@@ -1278,7 +1278,13 @@ class ConfigEntriesFlowManager(
         # a single config entry, but which already has an entry
         if (
             source not in {SOURCE_IGNORE, SOURCE_REAUTH, SOURCE_RECONFIGURE}
-            and self.config_entries.async_has_entries(handler, include_ignore=False)
+            and (
+                self.config_entries.async_has_entries(handler, include_ignore=False)
+                or (
+                    self.config_entries.async_has_entries(handler, include_ignore=True)
+                    and source != SOURCE_USER
+                )
+            )
             and await _support_single_config_entry_only(self.hass, handler)
         ):
             return ConfigFlowResult(
diff --git a/tests/components/mqtt/test_config_flow.py b/tests/components/mqtt/test_config_flow.py
index 5a95b9c5712..e99063b088b 100644
--- a/tests/components/mqtt/test_config_flow.py
+++ b/tests/components/mqtt/test_config_flow.py
@@ -444,7 +444,7 @@ async def test_hassio_ignored(hass: HomeAssistant) -> None:
     )
     assert result
     assert result.get("type") is FlowResultType.ABORT
-    assert result.get("reason") == "already_configured"
+    assert result.get("reason") == "single_instance_allowed"
 
 
 async def test_hassio_confirm(
diff --git a/tests/test_config_entries.py b/tests/test_config_entries.py
index 822dca559a8..700840eb90e 100644
--- a/tests/test_config_entries.py
+++ b/tests/test_config_entries.py
@@ -5729,6 +5729,14 @@ async def test_starting_config_flow_on_single_config_entry(
             None,
             {"type": data_entry_flow.FlowResultType.ABORT, "reason": "not_implemented"},
         ),
+        (
+            {"source": config_entries.SOURCE_ZEROCONF},
+            None,
+            {
+                "type": data_entry_flow.FlowResultType.ABORT,
+                "reason": "single_instance_allowed",
+            },
+        ),
     ],
 )
 async def test_starting_config_flow_on_single_config_entry_2(