Addressing the complex issues related to climate change requires multiple innovative approaches to identify research priorities involving multi-disciplinary research teams. Participatory approaches involving a variety of perspectives were used to gain insights into critical issues such as defining and understanding sustainable intensification, climate smart agriculture, and soil fertility prioritization in sub-Saharan Africa. This analysis drew on the foundation principles of participatory research and fundamental facilitation skills, while grounded in scientific knowledge and understanding of these complex issues. This approach essentially incorporates the relevant principles of participatory learning and action, primarily designed for development projects, with a new set of actors within the research and policy domain. The results of three case studies that utilized participatory techniques with a set of multi-disciplinary research teams are presented. The case studies include: 1) Feed the Future Sustainable Intensification Innovation Lab (SIIL) proposal development grounded in country-led and national priorities in Bangladesh, Tanzania, and Cambodia; 2) Climate Smart Agriculture and Sustainable Intensification (SI) Assessment and Priority Setting in Rwanda; and 3) Soil Fertility Prioritization in Sub Saharan Africa. We discuss how the future directions of such initiatives were shaped for improved outcomes.