diff --git a/qiskit/transpiler/passes/utils/gates_basis.py b/qiskit/transpiler/passes/utils/gates_basis.py
index 06943ea2d652..657b1d134852 100644
--- a/qiskit/transpiler/passes/utils/gates_basis.py
+++ b/qiskit/transpiler/passes/utils/gates_basis.py
@@ -12,6 +12,8 @@
 
 """Check if all gates in the DAGCircuit are in the specified basis gates."""
 
+from qiskit.circuit import ControlFlowOp
+from qiskit.converters import circuit_to_dag
 from qiskit.transpiler.basepasses import AnalysisPass
 
 
@@ -41,18 +43,32 @@ def run(self, dag):
             return
         gates_out_of_basis = False
         if self._target is not None:
+
+            def _visit_target(dag, wire_map):
+                for gate in dag.op_nodes():
+                    # Barrier is universal and supported by all backends
+                    if gate.name == "barrier":
+                        continue
+                    if not self._target.instruction_supported(
+                        gate.name, tuple(wire_map[bit] for bit in gate.qargs)
+                    ):
+                        return True
+                    # Control-flow ops still need to be supported, so don't skip them in the
+                    # previous checks.
+                    if isinstance(gate.op, ControlFlowOp):
+                        for block in gate.op.blocks:
+                            inner_wire_map = {
+                                inner: wire_map[outer]
+                                for outer, inner in zip(gate.qargs, block.qubits)
+                            }
+                            if _visit_target(circuit_to_dag(block), inner_wire_map):
+                                return True
+                return False
+
             qubit_map = {qubit: index for index, qubit in enumerate(dag.qubits)}
-            for gate in dag.op_nodes():
-                # Barrier is universal and supported by all backends
-                if gate.name == "barrier":
-                    continue
-                if not self._target.instruction_supported(
-                    gate.name, tuple(qubit_map[bit] for bit in gate.qargs)
-                ):
-                    gates_out_of_basis = True
-                    break
+            gates_out_of_basis = _visit_target(dag, qubit_map)
         else:
-            for gate in dag._op_names:
+            for gate in dag.count_ops(recurse=True):
                 if gate not in self._basis_gates:
                     gates_out_of_basis = True
                     break
diff --git a/test/python/transpiler/test_gates_in_basis_pass.py b/test/python/transpiler/test_gates_in_basis_pass.py
index 929ee7c89d93..bae16c921582 100644
--- a/test/python/transpiler/test_gates_in_basis_pass.py
+++ b/test/python/transpiler/test_gates_in_basis_pass.py
@@ -12,8 +12,8 @@
 
 """Test GatesInBasis pass."""
 
-from qiskit.circuit import QuantumCircuit
-from qiskit.circuit.library import HGate, CXGate, UGate
+from qiskit.circuit import QuantumCircuit, ForLoopOp, IfElseOp, Clbit
+from qiskit.circuit.library import HGate, CXGate, UGate, XGate, ZGate
 from qiskit.circuit.measure import Measure
 from qiskit.circuit.equivalence_library import SessionEquivalenceLibrary
 from qiskit.transpiler import PassManager
@@ -206,3 +206,60 @@ def test_all_gates_in_basis_after_translation_with_target(self):
         pm.append(analysis_pass)
         pm.run(circuit)
         self.assertTrue(pm.property_set["all_gates_in_basis"])
+
+    def test_basis_gates_control_flow(self):
+        """Test that the pass recurses into control flow."""
+        circuit = QuantumCircuit(4, 1)
+        circuit.h(0)
+        circuit.measure(0, 0)
+        with circuit.for_loop((1, 2)):
+            circuit.cx(0, 1)
+            with circuit.if_test((circuit.clbits[0], True)) as else_:
+                circuit.x(2)
+            with else_:
+                circuit.z(3)
+
+        one_missing = {"h", "measure", "for_loop", "cx", "if_else", "x"}
+        pass_ = GatesInBasis(one_missing)
+        pass_(circuit)
+        self.assertFalse(pass_.property_set["all_gates_in_basis"])
+
+        complete = one_missing | {"z"}
+        pass_ = GatesInBasis(complete)
+        pass_(circuit)
+        self.assertTrue(pass_.property_set["all_gates_in_basis"])
+
+    def test_basis_gates_target(self):
+        """Test that the pass recurses into control flow."""
+        circuit = QuantumCircuit(4, 1)
+        circuit.h(0)
+        circuit.measure(0, 0)
+        with circuit.for_loop((1, 2)):
+            circuit.cx(0, 1)
+            with circuit.if_test((circuit.clbits[0], True)) as else_:
+                circuit.x(2)
+            with else_:
+                circuit.z(3)
+
+        instructions = [
+            HGate(),
+            Measure(),
+            ForLoopOp((), None, QuantumCircuit(4)),
+            CXGate(),
+            IfElseOp((Clbit(), True), QuantumCircuit(2), QuantumCircuit(2)),
+            XGate(),
+            ZGate(),
+        ]
+        one_missing = Target(num_qubits=4)
+        for instruction in instructions[:-1]:
+            one_missing.add_instruction(instruction, {None: None})
+        pass_ = GatesInBasis(target=one_missing)
+        pass_(circuit)
+        self.assertFalse(pass_.property_set["all_gates_in_basis"])
+
+        complete = Target(num_qubits=4)
+        for instruction in instructions:
+            complete.add_instruction(instruction, {None: None})
+        pass_ = GatesInBasis(target=complete)
+        pass_(circuit)
+        self.assertTrue(pass_.property_set["all_gates_in_basis"])