diff --git a/qiskit/compiler/transpiler.py b/qiskit/compiler/transpiler.py
index 4d82214a5e03..d8a3be860321 100644
--- a/qiskit/compiler/transpiler.py
+++ b/qiskit/compiler/transpiler.py
@@ -645,6 +645,11 @@ def _parse_transpile_args(
             timing_constraints = target.timing_constraints()
         if backend_properties is None:
             backend_properties = target_to_backend_properties(target)
+    # If target is not specified and any hardware constraint object is
+    # manually specified then do not use the target from the backend as
+    # it is invalidated by a custom basis gate list or a custom coupling map
+    elif basis_gates is None and coupling_map is None:
+        target = _parse_target(backend, target)
 
     basis_gates = _parse_basis_gates(basis_gates, backend)
     initial_layout = _parse_initial_layout(initial_layout, circuits)
@@ -658,7 +663,6 @@ def _parse_transpile_args(
     callback = _parse_callback(callback, num_circuits)
     durations = _parse_instruction_durations(backend, instruction_durations, dt, circuits)
     timing_constraints = _parse_timing_constraints(backend, timing_constraints, num_circuits)
-    target = _parse_target(backend, target)
     if scheduling_method and any(d is None for d in durations):
         raise TranspilerError(
             "Transpiling a circuit with a scheduling method"
diff --git a/test/python/compiler/test_transpiler.py b/test/python/compiler/test_transpiler.py
index 8ede5702ae60..400662f30256 100644
--- a/test/python/compiler/test_transpiler.py
+++ b/test/python/compiler/test_transpiler.py
@@ -51,6 +51,7 @@
     FakeRueschlikon,
     FakeBoeblingen,
     FakeMumbaiV2,
+    FakeNairobiV2,
 )
 from qiskit.transpiler import Layout, CouplingMap
 from qiskit.transpiler import PassManager, TransformationPass
@@ -61,6 +62,7 @@
 from qiskit.transpiler.passmanager_config import PassManagerConfig
 from qiskit.transpiler.preset_passmanagers import level_0_pass_manager
 from qiskit.tools import parallel
+from qiskit.pulse import InstructionScheduleMap
 
 
 class CustomCX(Gate):
@@ -1899,3 +1901,73 @@ def run(self, dag):
         for qc_test in qcs_cal_added:
             added_cal = qc_test.calibrations["sx"][((0,), tuple())]
             self.assertEqual(added_cal, ref_cal)
+
+    @data(0, 1, 2, 3)
+    def test_backendv2_and_basis_gates(self, opt_level):
+        """Test transpile() with BackendV2 and basis_gates set."""
+        backend = FakeNairobiV2()
+        qc = QuantumCircuit(5)
+        qc.h(0)
+        qc.cz(0, 1)
+        qc.cz(0, 2)
+        qc.cz(0, 3)
+        qc.cz(0, 4)
+        qc.measure_all()
+        tqc = transpile(
+            qc,
+            backend=backend,
+            basis_gates=["u", "cz"],
+            optimization_level=opt_level,
+            seed_transpiler=12345678942,
+        )
+        op_count = set(tqc.count_ops())
+        self.assertEqual({"u", "cz", "measure", "barrier"}, op_count)
+        for inst in tqc.data:
+            if inst.operation.name not in {"u", "cz"}:
+                continue
+            qubits = tuple(tqc.find_bit(x).index for x in inst.qubits)
+            self.assertIn(qubits, backend.target.qargs)
+
+    @data(0, 1, 2, 3)
+    def test_backendv2_and_coupling_map(self, opt_level):
+        """Test transpile() with custom coupling map."""
+        backend = FakeNairobiV2()
+        qc = QuantumCircuit(5)
+        qc.h(0)
+        qc.cz(0, 1)
+        qc.cz(0, 2)
+        qc.cz(0, 3)
+        qc.cz(0, 4)
+        qc.measure_all()
+        cmap = CouplingMap.from_line(5, bidirectional=False)
+        tqc = transpile(
+            qc,
+            backend=backend,
+            coupling_map=cmap,
+            optimization_level=opt_level,
+            seed_transpiler=12345678942,
+        )
+        op_count = set(tqc.count_ops())
+        self.assertTrue({"rz", "sx", "x", "cx", "measure", "barrier"}.issuperset(op_count))
+        for inst in tqc.data:
+            if len(inst.qubits) == 2:
+                qubit_0 = tqc.find_bit(inst.qubits[0]).index
+                qubit_1 = tqc.find_bit(inst.qubits[1]).index
+                self.assertEqual(qubit_1, qubit_0 + 1)
+
+    @data(0, 1, 2, 3)
+    def test_backend_and_custom_gate(self, opt_level):
+        """Test transpile() with BackendV2, custom basis pulse gate."""
+        backend = FakeNairobiV2()
+        inst_map = InstructionScheduleMap()
+        inst_map.add("newgate", [0, 1], pulse.ScheduleBlock())
+        newgate = Gate("newgate", 2, [])
+        circ = QuantumCircuit(2)
+        circ.append(newgate, [0, 1])
+        tqc = transpile(
+            circ, backend, inst_map=inst_map, basis_gates=["newgate"], optimization_level=opt_level
+        )
+        self.assertEqual(len(tqc.data), 1)
+        self.assertEqual(tqc.data[0].operation, newgate)
+        qubits = tuple(tqc.find_bit(x).index for x in tqc.data[0].qubits)
+        self.assertIn(qubits, backend.target.qargs)