In the humid tropics, the rapid rate of deforestation has resulted in a race to protect remaining forest patches that are increasingly isolated within a rapidly expanding agricultural matrix. In these landscapes, a significant area consists of complex agro-forestry systems with high structural and functional plant diversity, providing critical resources for biodiversity conservation, such as food and habitat. Although not a substitute for natural forests, these anthropogenic habitats are gaining increasing conservation value as deforestation progresses. Shaded tree crops, such as cocoa, provide habitats for numerous forest dependent species of high conservation value and play a largely undocumented role in providing other ecological services. Following previous work on the botanical composition and structural complexity of cocoa agroforests in Talamanca (Costa Rica), we assessed if differences in the vegetation composition and structure of 36 cocoa agroforests could affect the wild diversity of small mammals, amphibians, reptiles, soil and litter macro-invertebrates and epiphytes found on cocoa trees and associated plants. Results show that Alpha-diversity is not affected by changes in vegetation structure and composition, except for amphibians and epiphytes found on cocoa trees. However, five taxa among eight showed distinct species composition patterns when compared among cocoa-based agroforestry clusters and with forest control. We showed that beta-diversity assessment enhances our understanding of the effect of management intensification on species composition and on habitat quality. The proper design of the shade component in these AFS will certainly play a key role in segregating wild species hosted in these systems and will open a new field of research for the intensification of both cocoa and associated productions in these highly diverse systems.