diff --git a/qiskit_ibm_runtime/utils/utils.py b/qiskit_ibm_runtime/utils/utils.py
index 168f6c7f2..e7eed6d53 100644
--- a/qiskit_ibm_runtime/utils/utils.py
+++ b/qiskit_ibm_runtime/utils/utils.py
@@ -47,6 +47,34 @@ def is_simulator(backend: BackendV1 | BackendV2) -> bool:
     return getattr(backend, "simulator", False)
 
 
+def _is_isa_circuit_helper(circuit: QuantumCircuit, target: Target) -> str:
+    """
+    A section of is_isa_circuit, separated to allow recursive calls
+    within blocks of conditional operatiosn.
+    """
+    for instruction in circuit.data:
+        operation = instruction.operation
+
+        name = operation.name
+        qargs = tuple(circuit.find_bit(x).index for x in instruction.qubits)
+        if (
+            not target.instruction_supported(name, qargs)
+            and name != "barrier"
+            and not circuit.has_calibration_for(instruction)
+        ):
+            return (
+                f"The instruction {name} on qubits {qargs} is not supported by the target system."
+            )
+
+        if isinstance(operation, ControlFlowOp):
+            for sub_circ in operation.blocks:
+                sub_string = _is_isa_circuit_helper(sub_circ, target)
+                if sub_string:
+                    return sub_string
+
+    return ""
+
+
 def is_isa_circuit(circuit: QuantumCircuit, target: Target) -> str:
     """Checks if the circuit is an ISA circuit, meaning that it has a layout and that it
     only uses instructions that exist in the target.
@@ -64,18 +92,7 @@ def is_isa_circuit(circuit: QuantumCircuit, target: Target) -> str:
             f"but the target system requires {target.num_qubits} qubits."
         )
 
-    for instruction in circuit.data:
-        name = instruction.operation.name
-        qargs = tuple(circuit.find_bit(x).index for x in instruction.qubits)
-        if (
-            not target.instruction_supported(name, qargs)
-            and name != "barrier"
-            and not circuit.has_calibration_for(instruction)
-        ):
-            return (
-                f"The instruction {name} on qubits {qargs} is not supported by the target system."
-            )
-    return ""
+    return _is_isa_circuit_helper(circuit, target)
 
 
 def are_circuits_dynamic(circuits: List[QuantumCircuit], qasm_default: bool = True) -> bool:
diff --git a/test/unit/test_estimator.py b/test/unit/test_estimator.py
index f36e4b732..b0d3d8543 100644
--- a/test/unit/test_estimator.py
+++ b/test/unit/test_estimator.py
@@ -21,6 +21,7 @@
 from qiskit.primitives.containers.estimator_pub import EstimatorPub
 
 from qiskit_ibm_runtime import Estimator, Session, EstimatorV2, EstimatorOptions, IBMInputValueError
+from qiskit_ibm_runtime.fake_provider import FakeSherbrooke
 
 from .mock.fake_runtime_service import FakeRuntimeService
 from ..ibm_test_case import IBMTestCase
@@ -286,3 +287,22 @@ def test_estimator_validations(self):
         obs = []
         with self.assertRaisesRegex(ValueError, "Empty observables array is not allowed"):
             inst.run(pubs=[(circ, obs)])
+
+    def test_gate_not_in_target(self):
+        """Test exception when circuits contain gates that are not basis gates"""
+        backend = FakeSherbrooke()
+        estimator = EstimatorV2(backend=backend)
+        observable = SparsePauliOp("Z")
+
+        circ = QuantumCircuit(1, 1)
+        circ.x(0)
+        circ.measure(0, 0)
+        with circ.if_test((0, 1)):
+            with circ.if_test((0, 0)) as else_:
+                circ.x(0)
+            with else_:
+                circ.h(0)
+        circ.measure(0, 0)
+
+        with self.assertRaisesRegex(IBMInputValueError, " h "):
+            estimator.run(pubs=[(circ, observable)])