Over the past decades, smallholder sectors in developing countries have experienced extensive land use changes, resulting in deforestation and environmental degradation, while drivers of agricultural expansion vary significantly by local/country/regional contexts. Agroforestry has the potential to promote sustainable agricultural intensification and landscape restoration. Due to the significant heterogeneity in the smallholder systems in developing countries in terms of agro-ecological contexts and institutional/political settings, there are no silver-bullet agroforestry interventions in any situation. Understanding what drives deforestation and/or why and how farmers decide to adopt agroforestry technologies can be useful to guide tailoring technology packages to locally specific contexts. The International Centre for Research in Agroforestry (ICRAF), with World Agroforestry as a brand name, has led system research to enhance the contribution of agroforestry in transforming livelihoods and landscapes, and Japanese scientists have played a role. This paper provides an overview of the evolution of ICRAF’s research priorities over 40 years with special reference to the contribution of Japanese scientists. It discusses their significance in academic and policy contributions, understanding the causes of deforestation and its effects on people in Southeast Asia, and unpacking farmers’ decision- making processes in the adoption of agroforestry technologies in East Africa. The paper concludes with arguments on the way forward for agroforestry research.