Current patterns of global change are threatening the supply of agrarian ecosystem services on which human well-being depends. Within this context, agroecology has emerged within political and scientific arenas as a socially equitable and ecologically sustainable alternative to conventional agriculture. We performed a systematic literature review to explore how agroecology and the ecosystem services framework have been adopted together in the scientific literature, focusing on studies including empirical data on the effects of agroecological practices on the supply of ecosystem services. In our search, we combined terms related to agricultural practices and terms related to ecosystem services. A total of 179 scientific articles were analyzed. Most of the studies used a biophysical approach to evaluate ecosystem services, with regulating and provisioning services being more frequently analyzed than cultural services. More than half of the analyzed relationships between agroecological practices and ecosystem services were positive. Remarkably, our review showed that many of the ten elements of agroecology defined by the FAO have not been properly addressed in the literature. Finally, we identified research gaps and provided insights on where future research and policies should be focused in order to promote the transition towards sustainable agrarian social-ecological systems that increase the supply of ecosystem services while minimizing environmental impacts.