diff --git a/cirq-core/cirq/transformers/target_gatesets/compilation_target_gateset.py b/cirq-core/cirq/transformers/target_gatesets/compilation_target_gateset.py
index d63e7d09ac4..45801676282 100644
--- a/cirq-core/cirq/transformers/target_gatesets/compilation_target_gateset.py
+++ b/cirq-core/cirq/transformers/target_gatesets/compilation_target_gateset.py
@@ -170,10 +170,24 @@ def decompose_to_target_gateset(self, op: 'cirq.Operation', moment_idx: int) ->
         old_2q_gate_count = sum(1 for o in ops.flatten_to_ops(old_optree) if len(o.qubits) == 2)
         new_2q_gate_count = sum(1 for o in ops.flatten_to_ops(new_optree) if len(o.qubits) == 2)
         switch_to_new = (
-            any(op not in self for op in ops.flatten_to_ops(old_optree))
+            any(
+                protocols.num_qubits(op) == 2 and op not in self
+                for op in ops.flatten_to_ops(old_optree)
+            )
             or new_2q_gate_count < old_2q_gate_count
         )
-        return new_optree if switch_to_new else old_optree
+        if switch_to_new:
+            return new_optree
+        mapped_old_optree: List['cirq.OP_TREE'] = []
+        for old_op in ops.flatten_to_ops(old_optree):
+            if old_op in self:
+                mapped_old_optree.append(old_op)
+            else:
+                decomposed_op = self._decompose_single_qubit_operation(old_op, moment_idx)
+                if decomposed_op is None or decomposed_op is NotImplemented:
+                    return NotImplemented
+                mapped_old_optree.append(decomposed_op)
+        return mapped_old_optree
 
     def _decompose_single_qubit_operation(
         self, op: 'cirq.Operation', moment_idx: int
diff --git a/cirq-core/cirq/transformers/target_gatesets/compilation_target_gateset_test.py b/cirq-core/cirq/transformers/target_gatesets/compilation_target_gateset_test.py
index c0fd64cd90c..c3af371e90f 100644
--- a/cirq-core/cirq/transformers/target_gatesets/compilation_target_gateset_test.py
+++ b/cirq-core/cirq/transformers/target_gatesets/compilation_target_gateset_test.py
@@ -199,3 +199,23 @@ def test_two_qubit_compilation_merge_and_replace_inefficient_component():
 m: ═════════════════════════════════════════════════════@═══^═══
 ''',
     )
+
+
+def test_two_qubit_compilation_replaces_only_if_2q_gate_count_is_less():
+    class DummyTargetGateset(cirq.TwoQubitCompilationTargetGateset):
+        def __init__(self):
+            super().__init__(cirq.X, cirq.CNOT)
+
+        def _decompose_two_qubit_operation(self, op: 'cirq.Operation', _) -> DecomposeResult:
+            q0, q1 = op.qubits
+            return [cirq.X.on_each(q0, q1), cirq.CNOT(q0, q1)] * 10
+
+        def _decompose_single_qubit_operation(self, op: 'cirq.Operation', _) -> DecomposeResult:
+            return cirq.X(*op.qubits) if op.gate == cirq.Y else NotImplemented
+
+    q = cirq.LineQubit.range(2)
+    ops = [cirq.Y.on_each(*q), cirq.CNOT(*q), cirq.Z.on_each(*q)]
+    c_orig = cirq.Circuit(ops)
+    c_expected = cirq.Circuit(cirq.X.on_each(*q), ops[-2:])
+    c_new = cirq.optimize_for_target_gateset(c_orig, gateset=DummyTargetGateset())
+    cirq.testing.assert_same_circuits(c_new, c_expected)