I have had success by creating RequestParser instances for the nested objects. Parse the root object first as you normally would, then use the results to feed into the parsers for the nested objects.
The trick is the location argument of the add_argument method and the req argument of the parse_args method. They let you manipulate what the RequestParser looks at.
Here’s an example:
root_parser = reqparse.RequestParser()
root_parser.add_argument('id', type=int)
root_parser.add_argument('name', type=str)
root_parser.add_argument('nested_one', type=dict)
root_parser.add_argument('nested_two', type=dict)
root_args = root_parser.parse_args()
nested_one_parser = reqparse.RequestParser()
nested_one_parser.add_argument('id', type=int, location=('nested_one',))
nested_one_args = nested_one_parser.parse_args(req=root_args)
nested_two_parser = reqparse.RequestParser()
nested_two_parser.add_argument('id', type=int, location=('nested_two',))
nested_two_args = nested_two_parser.parse_args(req=root_args)