diff --git a/changelog.d/5509.misc b/changelog.d/5509.misc
new file mode 100644
index 0000000000..cc27cf2940
--- /dev/null
+++ b/changelog.d/5509.misc
@@ -0,0 +1 @@
+Fix "Unexpected entry in 'full_schemas'" log warning.
diff --git a/synapse/storage/prepare_database.py b/synapse/storage/prepare_database.py
index fc10b9534e..7c4e1dc7ec 100644
--- a/synapse/storage/prepare_database.py
+++ b/synapse/storage/prepare_database.py
@@ -133,7 +133,7 @@ def _setup_new_database(cur, database_engine):
             if ver <= SCHEMA_VERSION:
                 valid_dirs.append((ver, abs_path))
         else:
-            logger.warn("Unexpected entry in 'full_schemas': %s", filename)
+            logger.debug("Ignoring entry '%s' in 'full_schemas'", filename)
 
     if not valid_dirs:
         raise PrepareDatabaseException(