diff --git a/news/afe-uuid.rst b/news/afe-uuid.rst
new file mode 100644
index 000000000..976d8a6e6
--- /dev/null
+++ b/news/afe-uuid.rst
@@ -0,0 +1,25 @@
+**Added:**
+
+* <news item>
+
+**Changed:**
+
+* AFE Protocols (AbsoluteBindingProtocol and AbsoluteSolvationProtocol)
+  now assign a single uuid for all ProtocolUnits in a repeat rather than
+  separating the uuid by legs of the transformation. PR #1948
+
+**Deprecated:**
+
+* <news item>
+
+**Removed:**
+
+* <news item>
+
+**Fixed:**
+
+* <news item>
+
+**Security:**
+
+* <news item>
diff --git a/src/openfe/protocols/openmm_afe/equil_binding_afe_method.py b/src/openfe/protocols/openmm_afe/equil_binding_afe_method.py
index e5c6ee0a2..06dcbaed0 100644
--- a/src/openfe/protocols/openmm_afe/equil_binding_afe_method.py
+++ b/src/openfe/protocols/openmm_afe/equil_binding_afe_method.py
@@ -502,10 +502,9 @@ def _create(
 
         protocol_units: dict[str, list[gufe.ProtocolUnit]] = {"solvent": [], "complex": []}
 
-        for phase in ["solvent", "complex"]:
-            for i in range(self.settings.protocol_repeats):
-                repeat_id = int(uuid.uuid4())
-
+        for i in range(self.settings.protocol_repeats):
+            repeat_id = int(uuid.uuid4())
+            for phase in ["solvent", "complex"]:
                 setup = unit_classes[phase]["setup"](
                     protocol=self,
                     stateA=stateA,
diff --git a/src/openfe/protocols/openmm_afe/equil_solvation_afe_method.py b/src/openfe/protocols/openmm_afe/equil_solvation_afe_method.py
index f43383830..5b2069c0d 100644
--- a/src/openfe/protocols/openmm_afe/equil_solvation_afe_method.py
+++ b/src/openfe/protocols/openmm_afe/equil_solvation_afe_method.py
@@ -466,10 +466,9 @@ def _create(
 
         protocol_units: dict[str, list[gufe.ProtocolUnit]] = {"solvent": [], "vacuum": []}
 
-        for phase in ["solvent", "vacuum"]:
-            for i in range(self.settings.protocol_repeats):
-                repeat_id = int(uuid.uuid4())
-
+        for i in range(self.settings.protocol_repeats):
+            repeat_id = int(uuid.uuid4())
+            for phase in ["solvent", "vacuum"]:
                 setup = unit_classes[phase]["setup"](
                     protocol=self,
                     stateA=stateA,
diff --git a/src/openfe/tests/protocols/openmm_abfe/test_abfe_protocol.py b/src/openfe/tests/protocols/openmm_abfe/test_abfe_protocol.py
index ee69720d2..6ba27ca2b 100644
--- a/src/openfe/tests/protocols/openmm_abfe/test_abfe_protocol.py
+++ b/src/openfe/tests/protocols/openmm_abfe/test_abfe_protocol.py
@@ -158,8 +158,8 @@ def test_create_independent_repeat_ids(benzene_modifications, T4_protein_compone
         for u in dag.protocol_units:
             repeat_ids.add(u.inputs["repeat_id"])
 
-    # squashed by repeat_id, that's 2 sets of 6
-    assert len(repeat_ids) == 12
+    # squashed by repeat_id, that's 1 uuid per repeat
+    assert len(repeat_ids) == 6
 
 
 def test_mda_universe_error():
diff --git a/src/openfe/tests/protocols/openmm_ahfe/test_ahfe_protocol.py b/src/openfe/tests/protocols/openmm_ahfe/test_ahfe_protocol.py
index 0d2c27adc..a5193a530 100644
--- a/src/openfe/tests/protocols/openmm_ahfe/test_ahfe_protocol.py
+++ b/src/openfe/tests/protocols/openmm_ahfe/test_ahfe_protocol.py
@@ -142,8 +142,8 @@ def test_create_independent_repeat_ids(benzene_system):
         for u in dag.protocol_units:
             repeat_ids.add(u.inputs["repeat_id"])
 
-    # squashed by repeat_id, that's 2 sets of 6
-    assert len(repeat_ids) == 12
+    # squashed by repeat_id, that's 1 uuid by repeat
+    assert len(repeat_ids) == 6
 
 
 def _assert_num_forces(system, forcetype, number):