diff --git a/.changes/unreleased/Fixes-20250107-173719.yaml b/.changes/unreleased/Fixes-20250107-173719.yaml
new file mode 100644
index 00000000000..2d2310f1bac
--- /dev/null
+++ b/.changes/unreleased/Fixes-20250107-173719.yaml
@@ -0,0 +1,6 @@
+kind: Fixes
+body: Ensure warning about microbatch lacking filter inputs is always fired
+time: 2025-01-07T17:37:19.373261-06:00
+custom:
+  Author: QMalcolm
+  Issue: "11159"
diff --git a/core/dbt/parser/manifest.py b/core/dbt/parser/manifest.py
index ba42c6637d3..023c5db9300 100644
--- a/core/dbt/parser/manifest.py
+++ b/core/dbt/parser/manifest.py
@@ -513,6 +513,7 @@ def load(self) -> Manifest:
         self.check_for_spaces_in_resource_names()
         self.check_for_microbatch_deprecations()
         self.check_forcing_batch_concurrency()
+        self.check_microbatch_model_has_a_filtered_input()
 
         return self.manifest
 
@@ -1472,21 +1473,6 @@ def check_valid_microbatch_config(self):
                             f"Microbatch model '{node.name}' optional 'concurrent_batches' config must be of type `bool` if specified, but got: {type(concurrent_batches)})."
                         )
 
-                    # Validate upstream node event_time (if configured)
-                    has_input_with_event_time_config = False
-                    for input_unique_id in node.depends_on.nodes:
-                        input_node = self.manifest.expect(unique_id=input_unique_id)
-                        input_event_time = input_node.config.event_time
-                        if input_event_time:
-                            if not isinstance(input_event_time, str):
-                                raise dbt.exceptions.ParsingError(
-                                    f"Microbatch model '{node.name}' depends on an input node '{input_node.name}' with an 'event_time' config of invalid (non-string) type: {type(input_event_time)}."
-                                )
-                            has_input_with_event_time_config = True
-
-                    if not has_input_with_event_time_config:
-                        fire_event(MicrobatchModelNoEventTimeInputs(model_name=node.name))
-
     def check_forcing_batch_concurrency(self) -> None:
         if self.manifest.use_microbatch_batches(project_name=self.root_project.project_name):
             adapter = get_adapter(self.root_project)
@@ -1508,6 +1494,28 @@ def check_forcing_batch_concurrency(self) -> None:
                         )
                     )
 
+    def check_microbatch_model_has_a_filtered_input(self):
+        if self.manifest.use_microbatch_batches(project_name=self.root_project.project_name):
+            for node in self.manifest.nodes.values():
+                if (
+                    node.config.materialized == "incremental"
+                    and node.config.incremental_strategy == "microbatch"
+                ):
+                    # Validate upstream node event_time (if configured)
+                    has_input_with_event_time_config = False
+                    for input_unique_id in node.depends_on.nodes:
+                        input_node = self.manifest.expect(unique_id=input_unique_id)
+                        input_event_time = input_node.config.event_time
+                        if input_event_time:
+                            if not isinstance(input_event_time, str):
+                                raise dbt.exceptions.ParsingError(
+                                    f"Microbatch model '{node.name}' depends on an input node '{input_node.name}' with an 'event_time' config of invalid (non-string) type: {type(input_event_time)}."
+                                )
+                            has_input_with_event_time_config = True
+
+                    if not has_input_with_event_time_config:
+                        fire_event(MicrobatchModelNoEventTimeInputs(model_name=node.name))
+
     def write_perf_info(self, target_path: str):
         path = os.path.join(target_path, PERF_INFO_FILE_NAME)
         write_file(path, json.dumps(self._perf_info, cls=dbt.utils.JSONEncoder, indent=4))
diff --git a/tests/functional/microbatch/test_microbatch.py b/tests/functional/microbatch/test_microbatch.py
index 953b372b226..ef747138fbd 100644
--- a/tests/functional/microbatch/test_microbatch.py
+++ b/tests/functional/microbatch/test_microbatch.py
@@ -464,9 +464,11 @@ def test_run_with_event_time(self, project):
         assert len(catcher.caught_events) == 1
 
         # our partition grain is "day" so running the same day without new data should produce the same results
+        catcher.caught_events = []
         with patch_microbatch_end_time("2020-01-03 14:57:00"):
-            run_dbt(["run"])
+            run_dbt(["run"], callbacks=[catcher.catch])
         self.assert_row_count(project, "microbatch_model", 3)
+        assert len(catcher.caught_events) == 1
 
         # add next two days of data
         test_schema_relation = project.adapter.Relation.create(