diff --git a/changelog.d/10532.bugfix b/changelog.d/10532.bugfix
new file mode 100644
index 000000000000..5cea4bbbcaa2
--- /dev/null
+++ b/changelog.d/10532.bugfix
@@ -0,0 +1 @@
+Only report protocols that are implemented by at least one service, as required by the spec when handling `GET /_matrix/client/r0/thirdparty/protocols`.
\ No newline at end of file
diff --git a/synapse/handlers/appservice.py b/synapse/handlers/appservice.py
index 21a17cd2e834..7ab558912eab 100644
--- a/synapse/handlers/appservice.py
+++ b/synapse/handlers/appservice.py
@@ -406,7 +406,11 @@ def _merge_instances(infos: List[JsonDict]) -> JsonDict:
 
             return combined
 
-        return {p: _merge_instances(protocols[p]) for p in protocols.keys()}
+        return {
+            p: _merge_instances(protocols[p])
+            for p in protocols.keys()
+            if len(protocols[p]) > 0
+        }
 
     async def _get_services_for_event(
         self, event: EventBase