diff --git a/changelog.d/9291.doc b/changelog.d/9291.doc
new file mode 100644
index 0000000000..422acd3891
--- /dev/null
+++ b/changelog.d/9291.doc
@@ -0,0 +1 @@
+Add note to `auto_join_rooms` config option explaining existing rooms must be publicly joinable.
diff --git a/docs/sample_config.yaml b/docs/sample_config.yaml
index 0e323846fa..601a8338eb 100644
--- a/docs/sample_config.yaml
+++ b/docs/sample_config.yaml
@@ -1328,6 +1328,8 @@ account_threepid_delegates:
 # By default, any room aliases included in this list will be created
 # as a publicly joinable room when the first user registers for the
 # homeserver. This behaviour can be customised with the settings below.
+# If the room already exists, make certain it is a publicly joinable
+# room. The join rule of the room must be set to 'public'.
 #
 #auto_join_rooms:
 #  - "#example:example.com"
diff --git a/synapse/config/registration.py b/synapse/config/registration.py
index ac48913a0b..afb3e0b2a1 100644
--- a/synapse/config/registration.py
+++ b/synapse/config/registration.py
@@ -378,6 +378,8 @@ class RegistrationConfig(Config):
         # By default, any room aliases included in this list will be created
         # as a publicly joinable room when the first user registers for the
         # homeserver. This behaviour can be customised with the settings below.
+        # If the room already exists, make certain it is a publicly joinable
+        # room. The join rule of the room must be set to 'public'.
         #
         #auto_join_rooms:
         #  - "#example:example.com"