diff --git a/homeassistant/helpers/schema_config_entry_flow.py b/homeassistant/helpers/schema_config_entry_flow.py
index 20a5d8de5a8..dcf7f07bf6b 100644
--- a/homeassistant/helpers/schema_config_entry_flow.py
+++ b/homeassistant/helpers/schema_config_entry_flow.py
@@ -171,13 +171,37 @@ class SchemaCommonFlowHandler:
 
         if user_input is not None:
             # User input was validated successfully, update options
-            self._options.update(user_input)
+            self._update_and_remove_omitted_optional_keys(
+                self._options, user_input, data_schema
+            )
 
         if user_input is not None or form_step.schema is None:
             return await self._show_next_step_or_create_entry(form_step)
 
         return await self._show_next_step(step_id)
 
+    def _update_and_remove_omitted_optional_keys(
+        self,
+        values: dict[str, Any],
+        user_input: dict[str, Any],
+        data_schema: vol.Schema | None,
+    ) -> None:
+        values.update(user_input)
+        if data_schema and data_schema.schema:
+            for key in data_schema.schema:
+                if (
+                    isinstance(key, vol.Optional)
+                    and key not in user_input
+                    and not (
+                        # don't remove advanced keys, if they are hidden
+                        key.description
+                        and key.description.get("advanced")
+                        and not self._handler.show_advanced_options
+                    )
+                ):
+                    # Key not present, delete keys old value (if present) too
+                    values.pop(key, None)
+
     async def _show_next_step_or_create_entry(
         self, form_step: SchemaFlowFormStep
     ) -> FlowResult:
@@ -221,7 +245,9 @@ class SchemaCommonFlowHandler:
         if user_input:
             # We don't want to mutate the existing options
             suggested_values = copy.deepcopy(suggested_values)
-            suggested_values.update(user_input)
+            self._update_and_remove_omitted_optional_keys(
+                suggested_values, user_input, await self._get_schema(form_step)
+            )
 
         if data_schema.schema:
             # Make a copy of the schema with suggested values set to saved options
diff --git a/tests/helpers/test_schema_config_entry_flow.py b/tests/helpers/test_schema_config_entry_flow.py
index 0bc8e0f1ff3..7954b63b241 100644
--- a/tests/helpers/test_schema_config_entry_flow.py
+++ b/tests/helpers/test_schema_config_entry_flow.py
@@ -671,3 +671,80 @@ async def test_options_flow_state(hass: HomeAssistant) -> None:
         "idx_from_flow_state": "blublu",
         "option1": "blabla",
     }
+
+
+async def test_options_flow_omit_optional_keys(
+    hass: HomeAssistant, manager: data_entry_flow.FlowManager
+) -> None:
+    """Test handling of advanced options in options flow."""
+    manager.hass = hass
+
+    OPTIONS_SCHEMA = vol.Schema(
+        {
+            vol.Optional("optional_no_default"): str,
+            vol.Optional("optional_default", default="a very reasonable default"): str,
+            vol.Optional("advanced_no_default", description={"advanced": True}): str,
+            vol.Optional(
+                "advanced_default",
+                default="a very reasonable default",
+                description={"advanced": True},
+            ): str,
+        }
+    )
+
+    OPTIONS_FLOW: dict[str, SchemaFlowFormStep | SchemaFlowMenuStep] = {
+        "init": SchemaFlowFormStep(OPTIONS_SCHEMA)
+    }
+
+    class TestFlow(MockSchemaConfigFlowHandler, domain="test"):
+        config_flow = {}
+        options_flow = OPTIONS_FLOW
+
+    mock_integration(hass, MockModule("test"))
+    mock_entity_platform(hass, "config_flow.test", None)
+    config_entry = MockConfigEntry(
+        data={},
+        domain="test",
+        options={
+            "optional_no_default": "abc123",
+            "optional_default": "not default",
+            "advanced_no_default": "abc123",
+            "advanced_default": "not default",
+        },
+    )
+    config_entry.add_to_hass(hass)
+
+    # Start flow in basic mode
+    result = await hass.config_entries.options.async_init(config_entry.entry_id)
+    assert result["type"] == data_entry_flow.FlowResultType.FORM
+    assert list(result["data_schema"].schema.keys()) == [
+        "optional_no_default",
+        "optional_default",
+    ]
+
+    result = await hass.config_entries.options.async_configure(result["flow_id"], {})
+    assert result["type"] == data_entry_flow.FlowResultType.CREATE_ENTRY
+    assert result["data"] == {
+        "advanced_default": "not default",
+        "advanced_no_default": "abc123",
+        "optional_default": "a very reasonable default",
+    }
+
+    # Start flow in advanced mode
+    result = await hass.config_entries.options.async_init(
+        config_entry.entry_id, context={"show_advanced_options": True}
+    )
+    assert result["type"] == data_entry_flow.FlowResultType.FORM
+    assert list(result["data_schema"].schema.keys()) == [
+        "optional_no_default",
+        "optional_default",
+        "advanced_no_default",
+        "advanced_default",
+    ]
+
+    result = await hass.config_entries.options.async_configure(result["flow_id"], {})
+    assert result["type"] == data_entry_flow.FlowResultType.CREATE_ENTRY
+    assert result["data"] == {
+        "advanced_default": "a very reasonable default",
+        "optional_default": "a very reasonable default",
+    }