Transdisciplinary courses aimed at advancing competencies and skills for dealing with complex sustainability transition challenges are an important part of sustainability education. Such courses are critically important, as they prepare students for addressing complex and intertwined challenges our society is facing. Core qualities such courses often strive for are interactions between students and stakeholders, the collaboration of students from a variety of backgrounds, peer learning through activating interactions on different layers: in project groups and the entire class, and reflexive and exploratory learning when addressing open-ended transition challenges in iterative processes. Already now and even more in the future, the design and facilitation of such transdisciplinary courses will be happening in various remote digital and hybrid formats. This chapter describes ten design principles that can be used by teachers and facilitators of transdisciplinary courses in the ever-evolving hybrid environments. We illustrate how these design principles can be operationalised with the help of different facilitation techniques. The facilitation technique examples are taken from the university course “Transdisciplinary Approaches for System Innovations”, run at KTH Royal Institute of Technology in Stockholm. With the inevitable evolution of hybrid learning environments in the future, the proposed principles can serve as the basis for reimagining transdisciplinary courses. As digital tools provide new opportunities, these principles can also be taken forward with more radical ideas to efficiently foster collaborative and reflexive learning.