diff --git a/python/BioSimSpace/Process/_amber.py b/python/BioSimSpace/Process/_amber.py
index f9b5e21ca..aec4bc743 100644
--- a/python/BioSimSpace/Process/_amber.py
+++ b/python/BioSimSpace/Process/_amber.py
@@ -304,6 +304,7 @@ def _setup(self, **kwargs):
 
                     # Set the simulation box.
                     system.setBox(*_cubic(box_length))
+                    reference_system.setBox(*_cubic(box_length))
 
             # Apply SOMD1 compatibility to the perturbation.
             if (
@@ -322,6 +323,7 @@ def _setup(self, **kwargs):
         else:
             # Check for perturbable molecules and convert to the chosen end state.
             system = self._checkPerturbable(system)
+            reference_system = self._checkPerturbable(self._reference_system)
 
         # RST file (coordinates).
         try:
diff --git a/tests/Process/test_amber.py b/tests/Process/test_amber.py
index 18a23df2a..eb66b0d88 100644
--- a/tests/Process/test_amber.py
+++ b/tests/Process/test_amber.py
@@ -243,6 +243,17 @@ def test_backbone_restraint_mask_rna(rna_system):
     assert "   restraintmask=\"@P,C5',C3',O3',O5'\"," in config
 
 
+@pytest.mark.skipif(has_amber is False, reason="Requires AMBER to be installed.")
+def test_perturbable_restraint(perturbable_system):
+    """Test a free energy perturbation protocol."""
+
+    # Create a short minimisation prototocol with a restraint.
+    protocol = BSS.Protocol.Minimisation(steps=100, restraint="heavy")
+
+    # Run the process, check that it finished without error, and returns a system.
+    run_process(perturbable_system, protocol)
+
+
 def run_process(system, protocol, check_data=False):
     """Helper function to run various simulation protocols."""