diff --git a/tools/schemacode/bidsschematools/schema.py b/tools/schemacode/bidsschematools/schema.py
index 8a51725f1b..ee7bb32bef 100644
--- a/tools/schemacode/bidsschematools/schema.py
+++ b/tools/schemacode/bidsschematools/schema.py
@@ -197,6 +197,7 @@ def load_schema(schema_path=None):
     if not schema.rules:
         raise ValueError(f"rules subdirectory path not found in {schema_path}")
 
+    dereference(schema)
     dereference(schema)
     flatten_enums(schema)