diff --git a/synapse/storage/controllers/persist_events.py b/synapse/storage/controllers/persist_events.py
index 98600054d6..8124802418 100644
--- a/synapse/storage/controllers/persist_events.py
+++ b/synapse/storage/controllers/persist_events.py
@@ -644,25 +644,7 @@ class EventsPersistenceStorageController:
             # TODO: Add a table to track what state groups we're currently
             # inserting? There's a race where this transaction takes so long
             # that we delete the state groups we're inserting.
-            #
-            # NYARGH: We don't have access to the state store here? Do we do
-            # this a layer above? There's not *that* much happening here?
-
-            min_state_epoch = min(ctx.state_epoch for _, ctx in chunk)
-            state_groups = {
-                ctx.state_group
-                for _, ctx in chunk
-                if ctx.state_group and not ctx.rejected
-            }
-            state_groups.update(
-                ctx.state_group_before_event
-                for _, ctx in chunk
-                if ctx.state_group_before_event is not None
-            )
-            await self.state_store.mark_state_groups_as_used(
-                min_state_epoch,
-                state_groups,
-            )
+            await self.state_store.mark_state_groups_as_used(events_and_contexts)
 
             await self.persist_events_store._persist_events_and_state_updates(
                 room_id,
diff --git a/synapse/storage/databases/state/store.py b/synapse/storage/databases/state/store.py
index f6bbae9246..35c1f8e407 100644
--- a/synapse/storage/databases/state/store.py
+++ b/synapse/storage/databases/state/store.py
@@ -186,26 +186,34 @@ class StateGroupDataStore(StateBackgroundUpdateStore, SQLBaseStore):
     async def mark_state_groups_as_used(
         self, event_and_contexts: Collection[Tuple[EventBase, EventContext]]
     ) -> None:
-        min_state_epoch = min(ctx.state_epoch for _, ctx in event_and_contexts)
-        state_groups = {
-            ctx.state_group
-            for _, ctx in event_and_contexts
-            if ctx.state_group and not ctx.rejected
-        }
-        state_groups.update(
-            ctx.state_group_before_event
-            for _, ctx in event_and_contexts
-            if ctx.state_group_before_event is not None
-        )
+        referenced_state_groups = []
+        state_epochs = []
+        for event, ctx in event_and_contexts:
+            if ctx.rejected or event.internal_metadata.is_outlier():
+                continue
 
-        if not state_groups:
+            assert ctx.state_epoch is not None
+            assert ctx.state_group is not None
+
+            state_epochs.append(ctx.state_epoch)
+
+            referenced_state_groups.append(ctx.state_group)
+
+            if ctx.state_group_before_event:
+                referenced_state_groups.append(ctx.state_group_before_event)
+
+        if not referenced_state_groups:
+            # We don't reference any state groups, so nothing to do
             return
 
+        assert state_epochs  # If we have state groups we have a state epoch
+        min_state_epoch = min(state_epochs)
+
         await self.db_pool.runInteraction(
             "mark_state_groups_as_used",
             self._mark_state_groups_as_used_txn,
             min_state_epoch,
-            state_groups,
+            referenced_state_groups,
         )
 
     def _mark_state_groups_as_used_txn(
diff --git a/synapse/storage/schema/__init__.py b/synapse/storage/schema/__init__.py
index 934e1ccced..0b54728ea5 100644
--- a/synapse/storage/schema/__init__.py
+++ b/synapse/storage/schema/__init__.py
@@ -19,7 +19,7 @@
 #
 #
 
-SCHEMA_VERSION = 88  # remember to update the list below when updating
+SCHEMA_VERSION = 89  # remember to update the list below when updating
 """Represents the expectations made by the codebase about the database schema
 
 This should be incremented whenever the codebase changes its requirements on the