diff --git a/changelog.d/6637.feature b/changelog.d/6637.feature
new file mode 100644
index 000000000000..5228ebc1e5c8
--- /dev/null
+++ b/changelog.d/6637.feature
@@ -0,0 +1 @@
+Add an option to disable autojoining rooms for guest accounts.
diff --git a/docs/sample_config.yaml b/docs/sample_config.yaml
index b06394a2bd67..94e1ec698fab 100644
--- a/docs/sample_config.yaml
+++ b/docs/sample_config.yaml
@@ -1223,6 +1223,13 @@ account_threepid_delegates:
 #
 #autocreate_auto_join_rooms: true
 
+# When auto_join_rooms is specified, setting this flag to false prevents
+# guest accounts from being automatically joined to the rooms.
+#
+# Defaults to true.
+#
+#auto_join_rooms_for_guests: false
+
 
 ## Metrics ###
 
diff --git a/synapse/config/registration.py b/synapse/config/registration.py
index a9aa8c3737f7..fecced2d57ed 100644
--- a/synapse/config/registration.py
+++ b/synapse/config/registration.py
@@ -128,6 +128,7 @@ def read_config(self, config, **kwargs):
             if not RoomAlias.is_valid(room_alias):
                 raise ConfigError("Invalid auto_join_rooms entry %s" % (room_alias,))
         self.autocreate_auto_join_rooms = config.get("autocreate_auto_join_rooms", True)
+        self.auto_join_rooms_for_guests = config.get("auto_join_rooms_for_guests", True)
 
         self.enable_set_displayname = config.get("enable_set_displayname", True)
         self.enable_set_avatar_url = config.get("enable_set_avatar_url", True)
@@ -368,6 +369,13 @@ def generate_config_section(self, generate_secrets=False, **kwargs):
         # users cannot be auto-joined since they do not exist.
         #
         #autocreate_auto_join_rooms: true
+
+        # When auto_join_rooms is specified, setting this flag to false prevents
+        # guest accounts from being automatically joined to the rooms.
+        #
+        # Defaults to true.
+        #
+        #auto_join_rooms_for_guests: false
         """
             % locals()
         )
diff --git a/synapse/handlers/register.py b/synapse/handlers/register.py
index ffda09226c80..5c7113a3bb5b 100644
--- a/synapse/handlers/register.py
+++ b/synapse/handlers/register.py
@@ -244,7 +244,13 @@ def register_user(
                     fail_count += 1
 
         if not self.hs.config.user_consent_at_registration:
-            yield defer.ensureDeferred(self._auto_join_rooms(user_id))
+            if not self.hs.config.auto_join_rooms_for_guests and make_guest:
+                logger.info(
+                    "Skipping auto-join for %s because auto-join for guests is disabled",
+                    user_id,
+                )
+            else:
+                yield defer.ensureDeferred(self._auto_join_rooms(user_id))
         else:
             logger.info(
                 "Skipping auto-join for %s because consent is required at registration",
diff --git a/tests/handlers/test_register.py b/tests/handlers/test_register.py
index 1b7935cef202..ca32f993a35f 100644
--- a/tests/handlers/test_register.py
+++ b/tests/handlers/test_register.py
@@ -135,6 +135,16 @@ def test_register_mau_blocked(self):
             self.handler.register_user(localpart="local_part"), ResourceLimitError
         )
 
+    def test_auto_join_rooms_for_guests(self):
+        room_alias_str = "#room:test"
+        self.hs.config.auto_join_rooms = [room_alias_str]
+        self.hs.config.auto_join_rooms_for_guests = False
+        user_id = self.get_success(
+            self.handler.register_user(localpart="jeff", make_guest=True),
+        )
+        rooms = self.get_success(self.store.get_rooms_for_user(user_id))
+        self.assertEqual(len(rooms), 0)
+
     def test_auto_create_auto_join_rooms(self):
         room_alias_str = "#room:test"
         self.hs.config.auto_join_rooms = [room_alias_str]