Agroforestry systems potentially deliver win-win solutions to production and biodiversity conservation in the tropics, but they need to be adapted to farmers' needs. We reviewed the literature on functional roles of biodiversity and resilience in tropical agroforestry systems, and we evaluated the evidence base for the beneficial role of biodiversity on yield, and effects of farmer management practices. Most studies investigated the biodiversity of taxa assumed to have positive functions for farmers. Shaded commodities and shifting cultivation were the systems most frequently assessed. Half of studies investigated plants, while Hymenoptera and birds were other major groups. Many agroforests had lower diversity than forest, while less than half had higher diversity than agriculture. The effects of management within systems were rarely addressed, with shade level the most frequent factor. Papers on resilience, mainly from shifting cultivation systems, showed the positive influence of adjacent old-growth forest to biodiversity, and the negative effects of tillage. Better reporting of results for meta-analyses, and long-term experiments on key questions are needed to evaluate the potential of agroforestry more thoroughly.