diff --git a/feflow/protocols/nonequilibrium_cycling.py b/feflow/protocols/nonequilibrium_cycling.py
index de6fc059..7f63de80 100644
--- a/feflow/protocols/nonequilibrium_cycling.py
+++ b/feflow/protocols/nonequilibrium_cycling.py
@@ -1,6 +1,6 @@
 # Adapted from perses: https://github.com/choderalab/perses/blob/protocol-neqcyc/perses/protocols/nonequilibrium_cycling.py
 
-from typing import Optional, List, Dict, Any
+from typing import Optional, Any, Union
 from collections.abc import Iterable
 from itertools import chain
 
@@ -988,15 +988,24 @@ def _create(
         self,
         stateA: ChemicalSystem,
         stateB: ChemicalSystem,
-        mapping: Optional[dict[str, ComponentMapping]] = None,
+        mapping: Optional[Union[ComponentMapping, list[ComponentMapping]]] = None,
         extends: Optional[ProtocolDAGResult] = None,
     ) -> list[ProtocolUnit]:
-        # Handle parameters
-        if mapping is None:
-            raise ValueError("`mapping` is required for this Protocol")
+        from openfe.protocols.openmm_rfe.equil_rfe_methods import (
+            _validate_alchemical_components,
+        )
+        from openfe.protocols.openmm_utils import system_validation
+
         if extends:
             raise NotImplementedError("Can't extend simulations yet")
 
+        # Do manual validation until it is part of the protocol
+        # Get alchemical components & validate them + mapping
+        alchem_comps = system_validation.get_alchemical_components(stateA, stateB)
+        # raise an error if we have more than one mapping
+        _validate_alchemical_components(alchem_comps, mapping)
+        mapping = mapping[0] if isinstance(mapping, list) else mapping  # type: ignore
+
         # inputs to `ProtocolUnit.__init__` should either be `Gufe` objects
         # or JSON-serializable objects
         num_cycles = self.settings.num_cycles
diff --git a/feflow/tests/conftest.py b/feflow/tests/conftest.py
index 221eaeaa..fda42e02 100644
--- a/feflow/tests/conftest.py
+++ b/feflow/tests/conftest.py
@@ -221,8 +221,8 @@ def mapping_toluene_toluene(toluene):
         i: i for i in range(len(toluene.to_rdkit().GetAtoms()))
     }
     mapping_obj = LigandAtomMapping(
-        componentA=toluene,
-        componentB=toluene,
+        componentA=toluene.copy_with_replacements(name="toluene_a"),
+        componentB=toluene.copy_with_replacements(name="toluene_b"),
         componentA_to_componentB=mapping_toluene_to_toluene,
     )
     return mapping_obj
diff --git a/feflow/tests/test_nonequilibrium_cycling.py b/feflow/tests/test_nonequilibrium_cycling.py
index cbfaea8e..27b0d491 100644
--- a/feflow/tests/test_nonequilibrium_cycling.py
+++ b/feflow/tests/test_nonequilibrium_cycling.py
@@ -307,7 +307,13 @@ def test_create_execute_gather(
         ],
     )
     def test_create_execute_gather_toluene_to_toluene(
-        self, protocol, toluene_vacuum_system, mapping_toluene_toluene, tmpdir, request
+        self,
+        protocol,
+        toluene_vacuum_system,
+        mapping_toluene_toluene,
+        tmpdir,
+        request,
+        toluene,
     ):
         """
         Perform 20 independent simulations of the NEQ cycling protocol for the toluene to toluene
@@ -328,10 +334,16 @@ def test_create_execute_gather_toluene_to_toluene(
         import numpy as np
 
         protocol = request.getfixturevalue(protocol)
-
+        # rename the components
+        toluene_state_a = toluene_vacuum_system.copy_with_replacements(
+            components={"ligand": toluene.copy_with_replacements(name="toluene_a")}
+        )
+        toluene_state_b = toluene_vacuum_system.copy_with_replacements(
+            components={"ligand": toluene.copy_with_replacements(name="toluene_b")}
+        )
         dag = protocol.create(
-            stateA=toluene_vacuum_system,
-            stateB=toluene_vacuum_system,
+            stateA=toluene_state_a,
+            stateB=toluene_state_b,
             name="Toluene vacuum transformation",
             mapping=mapping_toluene_toluene,
         )
@@ -495,6 +507,27 @@ def test_failing_partial_charge_assign(
 
                 execute_DAG(dag, shared_basedir=shared, scratch_basedir=scratch)
 
+    def test_error_with_multiple_mappings(
+        self,
+        protocol_short,
+        benzene_vacuum_system,
+        toluene_vacuum_system,
+        mapping_benzene_toluene,
+    ):
+        """
+        Make sure that when a list of mappings is passed that an error is raised.
+        """
+
+        with pytest.raises(
+            ValueError, match="A single LigandAtomMapping is expected for this Protocol"
+        ):
+            _ = protocol_short.create(
+                stateA=benzene_vacuum_system,
+                stateB=toluene_vacuum_system,
+                name="Test protocol",
+                mapping=[mapping_benzene_toluene, mapping_benzene_toluene],
+            )
+
 
 class TestSetupUnit:
     def test_setup_user_charges(