Agroforestry systems are widely extolled as a biodiversity-friendly alternative to food and wood production. However, few studies on large-vertebrates in the tropics consistently support this assumption. In the Amazonian ‘arch of deforestation’, commodity cropland and pastures for beef production have relentlessly replaced native forests. Agroforestry should therefore be both economically profitable and a more wildlife-friendly land-use alternative. Here we assess the local abundance and habitat use by forest primates and ungulates in a landscape mosaic containing large areas of primary forest and teak (Tectona grandis) agroforestry. We focused on animals of these groups because they have similar day ranges and home ranges, and are at the same trophic level. We surveyed 12 transects in both of these environments, totalling 485 km walked. We recorded four ungulate (Tayassu pecari, Pecari tajacu, Mazama americana, and Tapirus terrestris) and seven primate species (Ateles chamek, Lagothrix cana, Sapajus apella, Saimiri ustus, Chiropotes albinasus, Plecturocebus cf. moloch and Mico cf. emiliae). We indicate the importance of a species-level approach to evaluate the contribution of agroforests to population persistence. Large-bodied atelids, which are ripe-fruit-pulp specialists, were never recorded in teak agroforest. Sakis were more common in primary forest, while the smallest faunivore-frugivores had similar sighting rates in both environments. Ungulates exhibited subtler differences in their use of space than primates, but their sighting rates and track counts indicated temporal niche partition. White-lipped peccaries and red brocket deer were the only ungulates more frequently recorded in primary forest areas. Teak agroforestry still harbours some large and midsized frugivores, which may contribute with some biotic ecosystem services if their patches are connected to primary tropical forests. However, teak agroforestry should not be used to justify population subsidies for all Amazonian forest vertebrate species, since at least some threatened species clearly avoid forest stands dominated by this fast-growing exotic tree.