The production of sufficient food for an increasing global population while conserving natural capital is a major challenge to humanity. Tree-mediated ecosystem services are recognized as key features of more sustainable agroecosystems but the strategic management of tree attributes for ecosystem service provision is poorly understood. Six agroforestry and tree cover transition studies, spanning tropical/subtropical forest zones in three continents, were synthesized to assess the contribution of tree cover to the conservation of biodiversity and ecosystem services. Loss of native earthworm populations resulted in 76% lower soil macroporosity when shade trees were absent in coffee agriculture. Increased tree cover contributed to 53% increase in tea crop yield, maintained 93% of crop pollinators found in the natural forest and, in combination with nearby forest fragments, contributed to as much as 86% lower incidence for coffee berry borer. In certain contexts, shade trees contributed to negative effects resulting from increases in abundance of white stem borer and lacebugs and resulted in 60% reduction of endangered tree species compared to forest. Managing trees for ecosystem services requires understanding which tree species to include and how to manage them for different socio-ecological contexts. This knowledge needs to be shared and translated into viable options with farming communities.