Following severe forest loss in recent decades, Southeast Asian countries are increasingly employing social forestry as a means to ensure the sustainable development of their forest-dwelling communities. Given the potential of agroforestry to provide multiple ecosystem services, habitat for the maintenance of biodiversity, and the economic and social development of communities that cultivate them, many civil society organizations and NGOs involved are turning to agroforestry to achieve the goals of social forestry. However, implementing agroforesty per se may not be sufficient if agroforestry systems are not adequately diversified to meet management goals and limited tools exist that facilitate appropriate species selection in diversification. Here we review the potential of diversified agroforestry for social forestry and similar schemes, critically evaluating its advantages and challenges, before detailing two methodological tools, one based on functional traits and the other phylogeny, that may aid in generating recommendations for the effective diversification of agroforestry. Diversified agroforestry was found to have great potential as a sustainable, multifunctional land-use that is predominantly held back by the availability of resources, technical aid and tailored market access. Appropriate species selection may be a bottle-neck that can be alleviated by the tools presented. The first tool enables comparable species (in this case woody species) to be delineated into functionally distinct groups from functional trait data, which is illustrated using data from agroforests in Central Kalimantan, Borneo. The second produces co-cultivation recommendations based on phylogenetic distances between species. The functional groups identified and the recommendations based on phylogenetic distance both correspond to product types and specific uses within agroforestry, further incentivizing on-farm income diversification due to additional environmental benefits. When applied appropriately, the tools presented would allow for the cultivation of complementary species that may lead to improved habitat and ecosystem service provision without compromising yields. When coupled with appropriate market mechanisms, cultivating diversified agroforests may ensure the sustainable use of land under social forestry in Southeast Asia. Additionally, the two tools presented here have applicability in silviculture, restoration and other agroecosystems worldwide.