diff --git a/cmake/ExternalDependencies.cmake b/cmake/ExternalDependencies.cmake
index cb960a7a..6e7964b9 100644
--- a/cmake/ExternalDependencies.cmake
+++ b/cmake/ExternalDependencies.cmake
@@ -22,7 +22,7 @@ endif()
 # cmake-format: off
 set(MQT_CORE_VERSION 2.7.1
     CACHE STRING "MQT Core version")
-set(MQT_CORE_REV "ee7482834c75c6ba7b5ce5fbd74829cb513e3c01"
+set(MQT_CORE_REV "04a1b371e1f4e52125471a610f0ed3cd1afe6b5d"
     CACHE STRING "MQT Core identifier (tag, branch or commit hash)")
 set(MQT_CORE_REPO_OWNER "cda-tum"
 	CACHE STRING "MQT Core repository owner (change when using a fork)")
diff --git a/src/EquivalenceCheckingManager.cpp b/src/EquivalenceCheckingManager.cpp
index dd4614c7..ba2b8591 100644
--- a/src/EquivalenceCheckingManager.cpp
+++ b/src/EquivalenceCheckingManager.cpp
@@ -189,6 +189,10 @@ void EquivalenceCheckingManager::setupAncillariesAndGarbage() {
   const auto qubitDifference =
       largerCircuit.getNqubits() - smallerCircuit.getNqubits();
 
+  if (qubitDifference == 0) {
+    return;
+  }
+
   std::vector<std::pair<qc::Qubit, std::optional<qc::Qubit>>> removed{};
   removed.reserve(qubitDifference);
 
diff --git a/test/python/test_verify.py b/test/python/test_verify.py
index 38fb1ff2..4287c6bd 100644
--- a/test/python/test_verify.py
+++ b/test/python/test_verify.py
@@ -93,3 +93,30 @@ def test_cpp_exception_propagation_internal() -> None:
 
     with pytest.raises(ValueError, match="Lookahead application scheme can only be used for matrices."):
         qcec.verify(qc, qc, configuration=config)
+
+
+def test_zx_ancilla_support() -> None:
+    """This is a regression test for the handling of ancilla registers in the ZX checker."""
+    from qiskit.circuit import AncillaRegister
+
+    anc = AncillaRegister(1)
+
+    qc1 = QuantumCircuit(1, 0)
+
+    qc1.add_register(anc)
+    qc1.h(anc[0])
+
+    qc2 = QuantumCircuit(1, 0)
+    qc2.add_register(anc)
+
+    result = qcec.verify(
+        qc1,
+        qc2,
+        check_partial_equivalence=True,
+        parallel=False,
+        run_alternating_checker=False,
+        run_simulation_checker=False,
+        run_zx_checker=True,
+        run_construction_checker=False,
+    )
+    assert result.equivalence == qcec.EquivalenceCriterion.not_equivalent
diff --git a/test/test_zx.cpp b/test/test_zx.cpp
index 60937782..cd00b8e9 100644
--- a/test/test_zx.cpp
+++ b/test/test_zx.cpp
@@ -449,3 +449,45 @@ TEST_F(ZXTest, TwoQubitRotations) {
   EXPECT_EQ(ecm->getResults().equivalence,
             ec::EquivalenceCriterion::Equivalent);
 }
+
+TEST_F(ZXTest, EmptyCircuitWithAncillas) {
+  auto qc1 = qc::QuantumComputation(0U);
+  qc1.addAncillaryRegister(1);
+  qc1.x(0);
+
+  auto qc2 = qc::QuantumComputation(0U);
+  qc2.addAncillaryRegister(1);
+
+  config.execution.runZXChecker = true;
+  config.execution.parallel = false;
+  config.execution.runSimulationChecker = false;
+  config.execution.runAlternatingChecker = false;
+  config.execution.runConstructionChecker = false;
+  ecm = std::make_unique<ec::EquivalenceCheckingManager>(qc1, qc2, config);
+
+  ecm->run();
+  EXPECT_EQ(ecm->getResults().equivalence,
+            ec::EquivalenceCriterion::NotEquivalent);
+}
+
+TEST_F(ZXTest, EmptyCircuitWithAncillasAndGarbage) {
+  auto qc1 = qc::QuantumComputation(1U);
+  qc1.addAncillaryRegister(1);
+  qc1.setLogicalQubitGarbage(1);
+  qc1.h(1);
+
+  auto qc2 = qc::QuantumComputation(1U);
+  qc2.addAncillaryRegister(1);
+  qc2.setLogicalQubitGarbage(1);
+
+  config.execution.runZXChecker = true;
+  config.execution.parallel = false;
+  config.execution.runSimulationChecker = false;
+  config.execution.runAlternatingChecker = false;
+  config.execution.runConstructionChecker = false;
+  ecm = std::make_unique<ec::EquivalenceCheckingManager>(qc1, qc2, config);
+
+  ecm->run();
+  EXPECT_EQ(ecm->getResults().equivalence,
+            ec::EquivalenceCriterion::Equivalent);
+}