diff --git a/doc/releases/changelog-0.13.0.md b/doc/releases/changelog-0.13.0.md
index 1167e2296..3873df5f2 100644
--- a/doc/releases/changelog-0.13.0.md
+++ b/doc/releases/changelog-0.13.0.md
@@ -348,6 +348,11 @@
 for example the one-shot mid circuit measurement transform.
   [(#2056)](https://github.com/PennyLaneAI/catalyst/pull/2056)
 
+* Fixed a bug where applying a quantum transform after a QNode could produce incorrect results or 
+  errors in certain cases. This resolves issues related to transforms operating on QNodes with 
+  classical outputs and improves compatibility with measurement transforms.
+  [(#2081)](https://github.com/PennyLaneAI/catalyst/pull/2081)
+
 <h3>Internal changes ⚙️</h3>
 
 * Updates use of `qml.transforms.dynamic_one_shot.parse_native_mid_circuit_measurements` to improved signature.
diff --git a/frontend/catalyst/jax_tracer.py b/frontend/catalyst/jax_tracer.py
index 82325b780..06a7a7662 100644
--- a/frontend/catalyst/jax_tracer.py
+++ b/frontend/catalyst/jax_tracer.py
@@ -1257,15 +1257,13 @@ def apply_transforms(
             raise CompileError(msg)
         tracing_mode = TracingMode.TRANSFORM
     elif len(qnode_program) or have_measurements_changed(tape, tapes[0]):
-        # TODO: Ideally we should allow qnode transforms that don't modify the measurements to
-        # operate in the permissive tracing mode, but that currently leads to a small number of
-        # test failures due to the different result format produced in trace_quantum_function.
-        only_with_dynamic_one_shot = all(
-            "dynamic_one_shot_partial" in str(getattr(qnode, "transform", ""))
+        with_measurement_from_counts_or_samples = any(
+            "measurements_from_counts" in (transform_str := str(getattr(qnode, "transform", "")))
+            or "measurements_from_samples" in transform_str
             for qnode in qnode_program
         )
 
-        if has_classical_outputs(flat_results) and not only_with_dynamic_one_shot:
+        if has_classical_outputs(flat_results) and with_measurement_from_counts_or_samples:
             msg = (
                 "Transforming MeasurementProcesses is unsupported with non-MeasurementProcess "
                 "QNode outputs. The selected device, options, or applied QNode transforms, may be "
diff --git a/frontend/catalyst/qfunc.py b/frontend/catalyst/qfunc.py
index 38173c5ed..314137353 100644
--- a/frontend/catalyst/qfunc.py
+++ b/frontend/catalyst/qfunc.py
@@ -404,6 +404,8 @@ def _process_terminal_measurements(mcm_method, cpy_tape, out, snapshots, shot_ve
     """Process measurements when there are no mid-circuit measurements."""
     assert mcm_method == "one-shot"
 
+    # flatten the outs structure
+    out, _ = tree_flatten(out)
     new_out = []
     idx = 0
 
diff --git a/frontend/test/pytest/test_transform.py b/frontend/test/pytest/test_transform.py
index deda75533..b7aafd2ef 100644
--- a/frontend/test/pytest/test_transform.py
+++ b/frontend/test/pytest/test_transform.py
@@ -1103,7 +1103,7 @@ def inject_device_transforms(self, ctx, execution_config=None, shots=None):
 
             return program, config
 
-        # Simulate a Qrack-like device that requires meassurement process transforms.
+        # Simulate a Qrack-like device that requires measurement process transforms.
         # Qnode transforms raise this error anyway so we cannot use them directly.
         original_preprocess = QJITDevice.preprocess
         monkeypatch.setattr(QJITDevice, "preprocess", inject_device_transforms)