The need to deal with complexity is getting increasingly attention in research for development projects implemented through transboundary research partnerships between organisations from the Global North and the Global South. However, less is known about aspects beyond the systems under study that still affect complexity in the research project. We conducted an experience capitalization of five transboundary research partnerships undertaking research in 14 countries in the Global South. We found that the combination of multiple contexts, the cultural and disciplinary diversity of the transboundary research partnerships, and the set of rules and proceedings from the funding mechanism affect the levels of complexity. We further identified that a transdisciplinary approach and several related practices, like intercultural communication or integrative partnerships, are promising ways of dealing with complexity. Current structures in research for development need to improve in order to fully use the potential of transdisciplinarity for sustainability transformation.