diff --git a/doc/releases/changelog-dev.md b/doc/releases/changelog-dev.md
index 3412e495bb..31a110e932 100644
--- a/doc/releases/changelog-dev.md
+++ b/doc/releases/changelog-dev.md
@@ -14,6 +14,9 @@
 
 <h3>Bug fixes 🐛</h3>
 
-<h3>Contributors ✍️</h3>
+* Resolves a bug where calling `qml.counts()` within complicated and/or nested return expressions did not return the correct `PyTreeDef`.
+  [(#1219)](https://github.com/PennyLaneAI/catalyst/pull/1219)
 
-This release contains contributions from (in alphabetical order):
\ No newline at end of file
+<h3>Contributors ✍️</h3>
+This release contains contributions from (in alphabetical order):
+Arjun Bhamra
diff --git a/frontend/catalyst/jax_tracer.py b/frontend/catalyst/jax_tracer.py
index 1bfb118626..b6f42fff91 100644
--- a/frontend/catalyst/jax_tracer.py
+++ b/frontend/catalyst/jax_tracer.py
@@ -844,6 +844,9 @@ def trace_quantum_measurements(
     """
     shots = get_device_shots(device)
     out_classical_tracers = []
+    # NOTE: Number of qml.counts() we hit, used to update our iteration variable to account
+    # for additional leaf PyTreeDef nodes.
+    num_counts = 0
 
     for i, o in enumerate(outputs):
         if isinstance(o, MeasurementProcess):
@@ -914,16 +917,8 @@ def trace_quantum_measurements(
                     results = (jnp.asarray(results[0], jnp.int64), results[1])
                 out_classical_tracers.extend(results)
                 counts_tree = tree_structure(("keys", "counts"))
-                meas_return_trees_children = out_tree.children()
-                if len(meas_return_trees_children):
-                    meas_return_trees_children[i] = counts_tree
-                    out_tree = out_tree.make_from_node_data_and_children(
-                        PyTreeRegistry(),
-                        out_tree.node_data(),
-                        meas_return_trees_children,
-                    )
-                else:
-                    out_tree = counts_tree
+                num_counts += 1
+                out_tree = replace_child_tree(out_tree, i + num_counts, counts_tree)
             elif isinstance(o, StateMP) and not isinstance(o, DensityMatrixMP):
                 assert using_compbasis
                 shape = (2**nqubits,)
@@ -941,6 +936,37 @@ def trace_quantum_measurements(
     return out_classical_tracers, out_tree
 
 
+def replace_child_tree(tree: PyTreeDef, index: int, subtree: PyTreeDef) -> PyTreeDef:
+    """
+    Replace the index-th leaf node in a left-to-right depth-first tree traversal of a PyTreeDef
+    with a given subtree.
+
+    Args:
+        tree (PyTreeDef): The original PyTree.
+        index (int): The index of the leaf node to replace.
+        subtree (PyTreeDef): The new subtree to replace the original leaf node with.
+
+    Returns:
+        PyTreeDef: The modified PyTree with the replaced leaf node.
+    """
+
+    def replace_node(node, idx):
+        if not node.children():
+            # Leaf node => update leaf node counter
+            idx[0] += 1
+            if idx[0] == index:
+                return subtree
+            return node
+
+        return node.make_from_node_data_and_children(
+            PyTreeRegistry(),
+            node.node_data(),
+            [replace_node(child, idx) for child in node.children()],
+        )
+
+    return replace_node(tree, [0])
+
+
 @debug_logger
 def is_transform_valid_for_batch_transforms(tape, flat_results):
     """Not all transforms are valid for batch transforms.
diff --git a/frontend/test/pytest/test_pytree_args.py b/frontend/test/pytest/test_pytree_args.py
index b8f1ab1e61..ff55b45a81 100644
--- a/frontend/test/pytest/test_pytree_args.py
+++ b/frontend/test/pytest/test_pytree_args.py
@@ -593,5 +593,169 @@ def classical(x):
         assert result.a == 4
 
 
+class TestPyTreesQmlCounts:
+    """Test QJIT workflows when using qml.counts in a return expression."""
+
+    def test_pytree_qml_counts_simple(self):
+        """Test if a single qml.counts() can be used and output correctly."""
+        dev = qml.device("lightning.qubit", wires=1, shots=20)
+
+        @qjit
+        @qml.qnode(dev)
+        def circuit(x):
+            qml.RX(x, wires=0)
+            return {"1": qml.counts()}
+
+        observed = circuit(0.5)
+        expected = {"1": (jnp.array((0, 1), dtype=jnp.int64), jnp.array((0, 3), dtype=jnp.int64))}
+
+        _, expected_shape = tree_flatten(expected)
+        _, observed_shape = tree_flatten(observed)
+        assert expected_shape == observed_shape
+
+    def test_pytree_qml_counts_nested(self):
+        """Test if nested qml.counts() can be used and output correctly."""
+        dev = qml.device("lightning.qubit", wires=1, shots=20)
+
+        @qjit
+        @qml.qnode(dev)
+        def circuit(x):
+            qml.RX(x, wires=0)
+            return {"1": qml.counts()}, {"2": qml.expval(qml.Z(0))}
+
+        observed = circuit(0.5)
+        expected = (
+            {"1": (jnp.array((0, 1), dtype=jnp.int64), jnp.array((0, 3), dtype=jnp.int64))},
+            {"2": jnp.array(-1, dtype=jnp.float64)},
+        )
+
+        _, expected_shape = tree_flatten(expected)
+        _, observed_shape = tree_flatten(observed)
+        assert expected_shape == observed_shape
+
+        @qjit
+        @qml.qnode(dev)
+        def circuit2(x):
+            qml.RX(x, wires=0)
+            return [{"1": qml.expval(qml.Z(0))}, {"2": qml.counts()}], {"3": qml.expval(qml.Z(0))}
+
+        observed = circuit2(0.5)
+        expected = (
+            [
+                {"1": jnp.array(-1, dtype=jnp.float64)},
+                {"2": (jnp.array((0, 1), dtype=jnp.int64), jnp.array((0, 3), dtype=jnp.int64))},
+            ],
+            {"3": jnp.array(-1, dtype=jnp.float64)},
+        )
+        _, expected_shape = tree_flatten(expected)
+        _, observed_shape = tree_flatten(observed)
+        assert expected_shape == observed_shape
+
+    def test_pytree_qml_counts_2_nested(self):
+        """Test if multiple nested qml.counts() can be used and output correctly."""
+        dev = qml.device("lightning.qubit", wires=1, shots=20)
+
+        @qjit
+        @qml.qnode(dev)
+        def circuit(x):
+            qml.RX(x, wires=0)
+            return [{"1": qml.expval(qml.Z(0))}, {"2": qml.counts()}], [
+                {"3": qml.expval(qml.Z(0))},
+                {"4": qml.counts()},
+            ]
+
+        observed = circuit(0.5)
+        expected = (
+            [
+                {"1": jnp.array(-1, dtype=jnp.float64)},
+                {"2": (jnp.array((0, 1), dtype=jnp.int64), jnp.array((0, 3), dtype=jnp.int64))},
+            ],
+            [
+                {"3": jnp.array(-1, dtype=jnp.float64)},
+                {"4": (jnp.array((0, 1), dtype=jnp.int64), jnp.array((0, 3), dtype=jnp.int64))},
+            ],
+        )
+        _, expected_shape = tree_flatten(expected)
+        _, observed_shape = tree_flatten(observed)
+        assert expected_shape == observed_shape
+
+        @qjit
+        @qml.qnode(dev)
+        def circuit2(x):
+            qml.RX(x, wires=0)
+            return [{"1": qml.expval(qml.Z(0))}, {"2": qml.counts()}], [
+                {"3": qml.counts()},
+                {"4": qml.expval(qml.Z(0))},
+            ]
+
+        observed = circuit2(0.5)
+        expected = (
+            [
+                {"1": jnp.array(-1, dtype=jnp.float64)},
+                {"2": (jnp.array((0, 1), dtype=jnp.int64), jnp.array((0, 3), dtype=jnp.int64))},
+            ],
+            [
+                {"3": (jnp.array((0, 1), dtype=jnp.int64), jnp.array((0, 3), dtype=jnp.int64))},
+                {"4": jnp.array(-1, dtype=jnp.float64)},
+            ],
+        )
+        _, expected_shape = tree_flatten(expected)
+        _, observed_shape = tree_flatten(observed)
+        assert expected_shape == observed_shape
+
+    def test_pytree_qml_counts_longer(self):
+        """Test if 3 differently nested qml.counts() can be used and output correctly."""
+        dev = qml.device("lightning.qubit", wires=1, shots=20)
+
+        @qjit
+        @qml.qnode(dev)
+        def circuit(x):
+            qml.RX(x, wires=0)
+            return [
+                [{"1": qml.expval(qml.Z(0))}, {"2": qml.counts()}],
+                [{"3": qml.expval(qml.Z(0))}, {"4": qml.counts()}],
+                {"5": qml.expval(qml.Z(0))},
+                {"6": qml.counts()},
+            ]
+
+        observed = circuit(0.5)
+        expected = [
+            [
+                {"1": jnp.array(-1, dtype=jnp.float64)},
+                {"2": (jnp.array((0, 1), dtype=jnp.int64), jnp.array((0, 3), dtype=jnp.int64))},
+            ],
+            [
+                {"3": jnp.array(-1, dtype=jnp.float64)},
+                {"4": (jnp.array((0, 1), dtype=jnp.int64), jnp.array((0, 3), dtype=jnp.int64))},
+            ],
+            {"5": jnp.array(-1, dtype=jnp.float64)},
+            {"6": (jnp.array((0, 1), dtype=jnp.int64), jnp.array((0, 3), dtype=jnp.int64))},
+        ]
+        _, expected_shape = tree_flatten(expected)
+        _, observed_shape = tree_flatten(observed)
+        assert expected_shape == observed_shape
+
+    def test_pytree_qml_counts_mcm(self):
+        """Test qml.counts() with mid-circuit measurement."""
+        dev = qml.device("lightning.qubit", wires=1, shots=20)
+
+        @qml.qjit
+        @qml.qnode(dev, mcm_method="one-shot", postselect_mode=None)
+        def circuit(x):
+            qml.RX(x, wires=0)
+            measure(0, postselect=1)
+            return {"hi": qml.counts()}, {"bye": qml.expval(qml.Z(0))}, {"hi": qml.counts()}
+
+        observed = circuit(0.5)
+        expected = (
+            {"hi": (jnp.array((0, 1), dtype=jnp.int64), jnp.array((0, 3), dtype=jnp.int64))},
+            {"bye": jnp.array(-1, dtype=jnp.float64)},
+            {"hi": (jnp.array((0, 1), dtype=jnp.int64), jnp.array((0, 3), dtype=jnp.int64))},
+        )
+        _, expected_shape = tree_flatten(expected)
+        _, observed_shape = tree_flatten(observed)
+        assert expected_shape == observed_shape
+
+
 if __name__ == "__main__":
     pytest.main(["-x", __file__])