The establishment of planted trees and the natural regeneration of trees in agroecosystems is challenging. This study evaluated the establishment and natural regeneration of the following six native tree species in two agricultural systems in the Atlantic Forest in Paraguay: Cedrela fissilis Vell., Cordia trichotoma (Vell) Arráb. ex Steud., Handroanthus albus (Cham.) Mattos, Handroanthus impetiginosus (Mart. ex DC.) Mattos, Peltophorum dubium (Sprengel) Taubert, and Cordia americana (L.) Gottschling and J.S.Mill. At the study site in Caaguazú, 18 plots of 100 m2 each were established in 2 agronomic systems (conventional or agroecological) featuring 3 plantation types (pathsides, agricultural field edges, and islets). Trees were planted at this site in spring 2010 at a density of 1800 individuals ha−1, and the site was monitored for six years. At the study site in Itapúa, 30 plots of 50 m2 each were established in three agronomic systems (conventional, traditional, or agroecological). Trees were planted at this site in spring 2012 at a density of 1600 individuals ha−1, and the site was monitored for four years. Survival and relative growth rates of the planted species and natural regeneration were analyzed using generalized linear mixed models that considered species, agronomic system, and plantation type as fixed factors, and time and plot as random factors. At both sites, survival varied among species. Here, C. fissilis showed lower survival and C. trichotoma higher growth than the other species. Naturally regenerated species were C. trichotoma, H. albus, and P. dubium. The agronomic system and species affected growth and natural regeneration at both locations. Plantation type affected survival and growth in Caaguazú only. We conclude that species contributes more than agronomic system or plantation type to determining the survival, relative growth rate, and natural regeneration in agroforestry systems in the Paraguayan Atlantic Forest.