diff --git a/backends/qualcomm/_passes/layout_transform.py b/backends/qualcomm/_passes/layout_transform.py
index 64fabe5604e..f2bb7a45f3c 100644
--- a/backends/qualcomm/_passes/layout_transform.py
+++ b/backends/qualcomm/_passes/layout_transform.py
@@ -354,6 +354,14 @@ def call(self, graph_module: torch.fx.GraphModule):
                     self.traverse(node, graph_module)
             self.insert_permute, self.transformed_tag = True, QCOM_AXIS_ORDER
 
+            for node in graph.nodes:
+                if hasattr(node, "meta"):
+                    # Pop QCOM_AXIS_ORDER written by the to-edge LayoutTransform pass.
+                    # Without this, the main for-loop below would see is_transformed_node=True
+                    # for every sensitive node (deepcopy carries the tag from to-edge) and
+                    # skip them entirely, so no permute nodes would ever be inserted.
+                    node.meta.pop(QCOM_AXIS_ORDER, "")
+
         for node in sensitive_nodes:
             if not self.is_transformed_node(node):
                 self.mark_as_transformed(node)
diff --git a/backends/qualcomm/qnn_preprocess.py b/backends/qualcomm/qnn_preprocess.py
index 7b5aace51b8..94c884be2a2 100644
--- a/backends/qualcomm/qnn_preprocess.py
+++ b/backends/qualcomm/qnn_preprocess.py
@@ -23,10 +23,7 @@
 from executorch.backends.qualcomm.serialization.qc_schema_serialize import (
     flatbuffer_to_option,
 )
-from executorch.backends.qualcomm.utils.constants import (
-    QCOM_AXIS_ORDER,
-    QCOM_TENSOR_NAME,
-)
+from executorch.backends.qualcomm.utils.constants import QCOM_TENSOR_NAME
 from executorch.backends.qualcomm.utils.qnn_manager_lifecycle import (
     get_current_qnn_manager,
 )
@@ -100,10 +97,6 @@ def _build_op_wrappers(
         use_mha2sha: bool,
         backend_type: QnnExecuTorchBackendType,
     ):
-        for node in edge_program.graph_module.graph.nodes:
-            if hasattr(node, "meta"):
-                # pop certain keys in meta for not affecting the passes in compilation
-                node.meta.pop(QCOM_AXIS_ORDER, "")
         # QNN Delegate Specific Passes
         graph_module = get_qnn_pass_manager_cls(
             backend_type
diff --git a/backends/qualcomm/tests/rework/passes/passes_helper.py b/backends/qualcomm/tests/rework/passes/passes_helper.py
index 5b5a1eec6c6..07ac3b36a73 100644
--- a/backends/qualcomm/tests/rework/passes/passes_helper.py
+++ b/backends/qualcomm/tests/rework/passes/passes_helper.py
@@ -300,13 +300,6 @@ def lower_preprocess_gm(
             quantizer=quantizer,
         )
         gm = edge_ep.graph_module
-        # Mirror qnn_preprocess.py: strip QCOM_AXIS_ORDER from all nodes
-        from executorch.backends.qualcomm.utils.constants import QCOM_AXIS_ORDER
-
-        for node in gm.graph.nodes:
-            if hasattr(node, "meta"):
-                node.meta.pop(QCOM_AXIS_ORDER, "")
-
         pm_cls = get_qnn_pass_manager_cls(backend_type)
         pass_classes = PassPipeline._slice_to_target(
             pm_cls.get_preprocess_passes(use_mha2sha=use_mha2sha),