The research-in-development (RinD) approach to agricultural research focuses on working closely with communities through multistakeholder engagement to strengthen capacities to design, plan, implement and adapt research in order to improve the lives and livelihoods of the resource-poor living in complex social-ecological systems. The approach requires researchers and implementing partners to learn new skills and build new capacities as they work in multistakeholder teams. Capacity development is central to programs utilizing RinD, both to ensure quality engagement with stakeholders and to enable capacity to innovate as an outcome. In this working paper, the authors share learning from the implementation of a systems approach to capacity development in the CGIAR Research Program on Aquatic Agricultural Systems (AAS) over 3 years in five geographies.