Post-dispersal seed removal by ground-foraging frugivores promotes secondary dispersal of large seeds, reducing seed predation and increasing recruitment and regeneration. We studied how habitat disturbance influences seed removal patterns in the large-seeded palm Phytelephas aequatorialis within three habitats forming a continuum of disturbance (agroforestry system, disturbed forest, and less-disturbed forest) using seed removal experiments and camera trapping. We tested whether seed removal rates, and both richness and composition of seed remover communities varied between the habitats. On average, 15 seeds were removed under each tree in the agroforestry system over seven days, which was significantly lower compared to the disturbed forest (18) and the less-disturbed forest (19). Eight mammal species were identified removing seeds in the three habitats. On average, one mammal species removed seeds at each station in the agroforestry system, which was significantly lower than the two species observed in the two forests. The composition of seed remover communities was significantly different between the three habitats. Our results suggest that the loss of forest cover in the agroforestry system has reduced the richness of seed removers, which subsequently caused decreased removal rates. Nevertheless, this habitat could still maintain effective seed dispersal events because spiny rats were important seed removers. Our camera trap data should be taken as preliminary because we could only identify less than half of the animals responsible for seed removal. This study highlights the importance of medium- and large-sized rodents for the removal and effective dispersal of large seeds in disturbed tropical habitats.