This article explores the application of design prototyping as a creative method to support collaborative processes within transdisciplinary sustainability research and to meet the challenges they pose. By drawing on discourses on integration, mutual learning and co-production, we identified six different interrelated challenges, concerning: (1) diversity; (2) communication; (3) power; (4) epistemology; (5) personal and team; and (6) focus. We applied design prototyping in four workshops that pertained to different phases of a transdisciplinary research process and represented typical collaborative research activities. Our analysis illustrates how design prototyping contributes to addressing the challenges of collaboration, thereby expanding the methodological canon of transdisciplinary research. In particular, it helps to create conditions for future-oriented transformations and their prerequisites, such as trust, common understanding and appreciation of the other. Consequently, we argue that design prototyping can be used to facilitate knowledge integration and collaboration among the variety of actors involved in transdisciplinary processes.