Scaffolding is becoming an increasingly common concept in transdisciplinary research. However, there is some uncertainty about what scaffolding as a practice means for the research process, other than the wide-ranging use of tools and facilitated methods. In this chapter, we start from a societal need to co-create knowledge for complex thinking on complex issues as we argue that learning is central and that scaffolding has an important role to play in promoting learning as both process and process outcome. The chapter examines scaffolding both as metaphor and practice, and how these perspectives of scaffolding have bearings on transdisciplinary projects. We build our discussion from two components: an imaginary walk on the construction site and diverse principles and practices for complex thinking taken from varying disciplinary discourse where collaborative processes are central. We continue by developing a model for scaffolding from a systemic approach - a learning system - based on previous learning models. The chapter concludes with a discussion on the promises and pitfalls of scaffolding in transdisciplinary research and how scaffolding opens new avenues for transdisciplinary processes.