We studied the botanical and structural composition of the woody vegetation present in 36 cocoa-AFS and four forest patches located on the Nicaraguan Atlantic slope. We set up a 1000 square meter plot (20x50 m) where we identified, counted and measured all trees with dbh 10 cm and we used a semi-structured interview process with 36 producers to investigate cacao agronomic management and the use and management of shade trees. Cacao plant density was 660 trees ha-1; the cocoa-AFS had a total of 521 individuals (145 trees ha-1) in 35 families, 57 genera and 70 species on 3.6 ha. Musaceae were the most abundant species (182 stems ha-1) followed by Cordia alliodora (22 trees ha-1), Bactris gasipaes (20 individuals ha-1) and Ryania speciosa (17 plants ha-1). In the forest patches we counted 869 trees (2173 trees ha-1) in 47 families, 80 genera and 90 species. The most abundant and common species in the forest plots were Ryania speciosa (173 plants ha-1), Piper aduncum (143 trees ha-1) and Parkinsonia aculeata (83 trees ha-1). The diversity of woody species associated with cacao lower than the tree diversity recorded in forest patches, although it is within the ranges measured in other Central American cocoa orchards. The horizontal structure of the tree vegetation in cocoa-AFS was markedly different from that of forest patches. Up to 25% of the tree species inventoried in forest patches were recorded for the cocoa-AFS. We suggest promoting the diversification of the cacao orchards and other areas of the farm with fruit trees and valuable timber trees and we recommend providing technical assistance to producers about the selection of species for shade, management of natural regeneration and the design and management of shade in cacao orchards.