The seeds of most tropical plants are dispersed by animals, many of which also act as seed predators. Shifts in animal community composition, such as those driven by the clearing of native vegetation, are therefore likely to drive changes in plant recruitment. We used manipulative experiments excluding ants, small rodents, and birds to quantify the relative impacts of these granivores on animal-dispersed pioneer trees (ADPT) in fragments of savanna vegetation and adjacent soy plantations in Brazil’s Cerrado. We found that ants were the main consumers of ADPT seeds, that the rates of seed removal varied with seed size, and that removal rates were higher in savanna fragments than in soy plantations. However, we also found significant interactions between habitat type, seed species, and the type of seed predator being excluded. Our results underscore how challenging it can be to predict the influence of human disturbances on the interactions between plant and animal communities. Because ants, rodents, and birds are Cerrado’s the main seed dispersers and granivores, seedling recruitment in Cerrado landscape mosaics will depend on how these distinct but related processes are each influenced by species-specific patterns of seed size and seed abundance.