While transdisciplinarity offers a way to tackle complex social-ecological challenges, transdisciplinary research is a challenging task in itself. The integration of research methods across academic disciplines, the collaboration between researchers and practitioners, and the need to balance societal and disciplinary academic impacts pose many difficulties even to experienced applied scientists and even more so to early-career researchers. Young scholars face particular problems, given their lack of longer-term experience and their still fragile position within academia. Drawing on existing literature, an early-career researcher workshop, and our own experience as junior research group leaders, we discuss specific challenges and respective solution strategies of transdisciplinary research within the context of sustainability.