diff --git a/dlt/extract/resource.py b/dlt/extract/resource.py
index 1f3f9d9cfb..bdebd14d47 100644
--- a/dlt/extract/resource.py
+++ b/dlt/extract/resource.py
@@ -470,11 +470,13 @@ def add_step(
             self._pipe.insert_step(item_transform, insert_at)
         return self
 
-    def _remove_incremental_step(self) -> None:
-        self._pipe.remove_by_type(Incremental, IncrementalResourceWrapper)
+    def _remove_incremental_step(self) -> int:
+        return self._pipe.remove_by_type(Incremental, IncrementalResourceWrapper)
 
     def set_incremental(
-        self, new_incremental: Union[Incremental[Any], IncrementalResourceWrapper]
+        self,
+        new_incremental: Union[Incremental[Any], IncrementalResourceWrapper],
+        insert_at: Optional[int] = None,
     ) -> Optional[Union[Incremental[Any], IncrementalResourceWrapper]]:
         """Set/replace the incremental transform for the resource.
 
@@ -508,7 +510,7 @@ def set_incremental(
             if new_incremental:
                 if not isinstance(new_incremental, IncrementalResourceWrapper):
                     new_incremental = Incremental.ensure_instance(new_incremental)
-                self.add_step(new_incremental)
+                self.add_step(new_incremental, insert_at=insert_at)
         return new_incremental
 
     def _set_hints(
@@ -519,7 +521,11 @@ def _set_hints(
         if not create_table_variant:
             # try to late assign incremental
             if table_schema_template.get("incremental") is not None:
-                self.set_incremental(table_schema_template["incremental"])
+                incremental_step_index = self._pipe.find(Incremental, IncrementalResourceWrapper)
+                self.set_incremental(
+                    table_schema_template["incremental"],
+                    insert_at=incremental_step_index if incremental_step_index >= 0 else None,
+                )
             elif incremental := self.incremental:
                 # set primary key as dedup key on new incremental
                 resource_primary_key = self._hints.get("primary_key")
@@ -685,7 +691,7 @@ def _set_explicit_args(
         except Exception:
             pass
 
-    def _eject_config(self) -> bool:
+    def _eject_config(self) -> tuple[bool, int]:
         """Unwraps the pipe generator step from config injection and incremental wrappers by restoring the original step.
 
         Removes the step with incremental wrapper. Should be used before a subsequent _inject_config is called on the
@@ -696,12 +702,16 @@ def _eject_config(self) -> bool:
         if not self._pipe.is_empty and not self._args_bound:
             orig_gen = getattr(self._pipe.gen, "__GEN__", None)
             if orig_gen:
-                self._remove_incremental_step()
+                incremental_step_index = self._remove_incremental_step()
                 self._pipe.replace_gen(orig_gen)
-                return True
-        return False
+                return True, incremental_step_index
+        return False, -1
 
-    def _inject_config(self, incremental_from_hints_override: Optional[bool] = None) -> Self:
+    def _inject_config(
+        self,
+        incremental_from_hints_override: Optional[bool] = None,
+        incremental_step_index: int = -1,
+    ) -> Self:
         """Wraps the pipe generation step in incremental and config injection wrappers and adds pipe step with
         Incremental transform.
         """
@@ -723,7 +733,10 @@ def _inject_config(self, incremental_from_hints_override: Optional[bool] = None)
                     ),
                 )
             incr_f = incremental.wrap(sig, gen)
-            self.set_incremental(incremental)
+            self.set_incremental(
+                incremental,
+                insert_at=incremental_step_index if incremental_step_index >= 0 else None,
+            )
         else:
             incr_f = gen
         resource_sections = (known_sections.SOURCES, self.section, self.name)
@@ -792,8 +805,12 @@ def _clone(
         # try to eject and then inject configuration and incremental wrapper when resource is cloned
         # this makes sure that a take config values from a right section and wrapper has a separated
         # instance in the pipeline
-        if cloned_r._eject_config():
-            cloned_r._inject_config(incremental_from_hints_override=incremental_from_hints)
+        ejected, incremental_step_index = cloned_r._eject_config()
+        if ejected:
+            cloned_r._inject_config(
+                incremental_from_hints_override=incremental_from_hints,
+                incremental_step_index=incremental_step_index,
+            )
         return cloned_r
 
     def _update_wrapper(self) -> None:
diff --git a/tests/extract/test_incremental.py b/tests/extract/test_incremental.py
index 97c804d9a2..9b60630f05 100644
--- a/tests/extract/test_incremental.py
+++ b/tests/extract/test_incremental.py
@@ -42,7 +42,7 @@
     IncrementalPrimaryKeyMissing,
 )
 from dlt.extract.incremental.lag import apply_lag
-from dlt.extract.items_transform import ValidateItem
+from dlt.extract.items_transform import MetricsItem, ValidateItem
 from dlt.extract.resource import DltResource
 from dlt.pipeline.exceptions import PipelineStepFailed
 from dlt.sources.helpers.transform import take_first
@@ -2969,6 +2969,34 @@ def updated_is_int(updated_at=dlt.sources.incremental("updated_at", initial_valu
     assert pip_ex.value.__cause__.cursor_path == "updated_at"
 
 
+def test_clone_preserves_inserted_step_after_hints_incremental() -> None:
+    @dlt.source
+    def my_source():
+        @dlt.resource
+        def events():
+            yield [
+                {"id": 1, "updated_at": 1},
+                {"id": 2, "updated_at": 2},
+                {"id": 3, "updated_at": 3},
+            ]
+
+        return events
+
+    def count_rows(items: TDataItems, meta: Any, metrics: Dict[str, Any]) -> None:
+        if isinstance(items, list):
+            metrics["row_count"] = metrics.get("row_count", 0) + len(items)
+
+    resource = my_source().events
+    resource.apply_hints(incremental=dlt.sources.incremental("updated_at", initial_value=2))
+    resource.add_metrics(count_rows, insert_at=len(resource._pipe))
+
+    assert resource._pipe.find(Incremental) < resource._pipe.find(MetricsItem)
+
+    cloned_resource = resource._clone()
+
+    assert cloned_resource._pipe.find(Incremental) < cloned_resource._pipe.find(MetricsItem)
+
+
 def test_incremental_merge_native_representation():
     incremental = Incremental(cursor_path="some_path", lag=10)  # type: ignore