diff --git a/changelog.d/7299.misc b/changelog.d/7299.misc
new file mode 100644
index 000000000000..fd72c1de19e7
--- /dev/null
+++ b/changelog.d/7299.misc
@@ -0,0 +1 @@
+Add a sanity-check in the StreamChangeCache to check that important data is not being overwritten.
diff --git a/synapse/util/caches/stream_change_cache.py b/synapse/util/caches/stream_change_cache.py
index 235f64049c95..a2f38593a029 100644
--- a/synapse/util/caches/stream_change_cache.py
+++ b/synapse/util/caches/stream_change_cache.py
@@ -126,6 +126,21 @@ def entity_has_changed(self, entity, stream_pos):
         """
         assert type(stream_pos) is int
 
+        # sanity-check that we are not going to overwrite existing data.
+        current = self._cache.get(stream_pos)
+        if current is not None:
+            if current != entity:
+                logger.error(
+                    "Stream %s: %s has already changed at %s",
+                    self.name,
+                    current,
+                    stream_pos,
+                )
+                raise NotImplementedError(
+                    "more than one entity changing at a stream position"
+                )
+            return
+
         if stream_pos > self._earliest_known_stream_pos:
             old_pos = self._entity_to_key.get(entity, None)
             if old_pos is not None: