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Human land use has extensively degraded ecosystems, leading to biodiversity losses and reducing the provision of ecosystem services (ES). Agroforestry systems have been recommended as a cost-effective strategy that integrates production and biodiversity conservation, yet few studies have quantified the capacity of agroforestry systems to conserve biodiversity and ES provision. Here we quantify the effects of different types of agroforestry systems on biodiversity and ES in the Brazilian Atlantic Forest. We compared values of biodiversity and ES in different agroforestry systems with those found in conventional production systems and in old-growth forests (reference ecosystem). We assessed 72 studies encompassing 143 study sites and 1700 quantitative comparisons. In general, agroforestry and conventional production systems had lower values of mean effect size for biodiversity and ES provision than the reference systems. However, biodiverse agroforestry systems had higher values of mean effect size for biodiversity and ES provision than simple agroforestry systems and conventional production systems. The use of biodiverse agroforestry systems as an alternative production system reduces biodiversity loss and the negative impact on ES in production areas. Agroforestry systems provide up to 45% and 65% more benefits for biodiversity and ES levels, respectively, than conventional production systems; however, these benefits differ according to the type of agroforestry system. Our findings provide empirical evidence that a biodiverse agroforestry system is the best option to enhance biodiversity and ES in degraded areas where production systems based on sustainable management of natural resources are allowed by law. Our results supportenvironmental public policies focused on environmentally-friendly land management practice and forest landscape restoration techniques.