Coffee agroecosystems are extremely important for biodiversity conservation and contribute to the economic well being of millions of producers. Dozens of studies have highlighted the importance of maintaining diverse coffee agroecosystems for protecting biodiversity. Coffee agroecosystem diversity is maintained by preserving high tree diversity and density, creating multiple canopy layers, and encouraging the growth of epiphytes. Maintenance of diverse coffee systems may further promote ecosystem services such as increased pest control, protection from disease outbreaks, enhanced pollination, increased connectivity between forest fragments, and mitigated effects of global change. Coffee management choices also strongly influence coffee yields and the alternative products provided from the shade trees which can contribute to farmer incomes. We present here results of a quantitative synthesis and meta-anlaysis of more than 30 studies examining the relationship between biodiversity of ants, birds, and plants and the specific characteristics of coffee management systems that strongly correlate with species richness, especially that of forest species. We also briefly summarize available information on ecosystem services and economic outputs from coffee agroecosystems. The results from these studies can provide researchers, conservationists, and managers with information about which management factors most strongly affect biodiversity, and how management for biodiversity may influence the availability of alternative products, the prevalence of pests and disease, and the variation of coffee yields. Based on these results, we discuss the potential for restoring degraded agricultural habitats into diverse agroforests with enhanced ecological and economic sustainability and provide successful examples from two tropical regions.