Agroforestry systems enable food production while potentially conserving biodiversity, but it is still unknown how their characteristics, matrix, and ecoregion affect diversity. We aim at understanding biodiversity patterns in agroforestry systems originated from areas with alternative land use and natural vegetation in tropical ecoregions. Through a systematic review, we detected differences between agroforestry systems with the two origins, such as crop type, management strategy, matrix, and ecoregion. Agroforestry systems with the two origins had lower plant richness, tree basal area, and canopy cover than reference areas. We did not find an effect of agroforestry systems on vertebrate richness and only those originated from areas with natural vegetation showed a negative effect on invertebrate richness. The factors affecting species richness varied between agroforestry systems with the two origins and among taxonomic groups. However, in general, agroforestry systems implemented with greater vegetation diversity, with crop types that form more complex vegetation structure, less intensive management, and more permeable matrices had positive effects on species richness. Last, the species richness in agroforestry systems did not increase with increasing natural plant richness of the different ecoregions. We recommend that management strategies that do not greatly modify vegetation structure and resource availability to animals, as well as landscape features that enable the movement of animals and propagules are adopted in agroforestry systems when they aim at environmental management. Importantly, we advocate for the strict prohibition of agroforestry systems implementation in areas with preserved native vegetation due to the negative effects on plant and invertebrate communities.