Changes in biodiversity and ecosystem services in terrestrial systems are being driven by the synergistic interactions between the loss of native vegetation and land-use intensification. Disentangling the influence of these two processes on species persistence is an important step towards reconciling conservation and agriculture production. We investigated how forest cover and management intensification affect the conservation value of cacao agroforests for mammals in an Atlantic forest landscape in southern Bahia, the most extensive area of diverse shaded cacao plantations in Brazil. Although both factors affected the distribution of mammal species, management intensification had a stronger effect, negatively affecting a larger number of species. Frequency of domestic dogs, an indirect aspect of management intensification, negatively affected four species and lower connectivity of shading trees decreased the use of cacao agroforests by three species of conservation concern. In comparison, the reduced forest cover negatively affected two species of conservation concern. Our results suggest that controlling domestic dog populations is particularly valuable for large mammal conservation in agroforestry mosaics, since it does not affect crop productivity. Improving shade cover within agroforests, on the other hand, should be implemented carefully, maintaining acceptable yield while promoting canopy connectivity and the recruitment of tree species used by forest dependent mammals. However, the importance of both local management intensification and local forest cover are likely to be context dependent, and changes in their relative importance are likely to occur with different levels of deforestation at the landscape scale.