The forests of southeastern Amazonia are highly threatened by disturbances such as fragmentation, understory fires and extreme climatic events. Large-bodied frugivores such as the lowland tapir (Tapirus terrestris) have the potential to offset this process, supporting natural forest regeneration by dispersing a variety of seeds over long distances to disturbed forests. However, we know little about their effectiveness as seed dispersers in degraded forest landscapes. Here, we investigate the seed dispersal function of lowland tapirs in Amazonian forests subject to a range of human (fire, fragmentation) and natural (extreme droughts, windstorms) disturbances, using a combination of field observations, camera traps, and Light Detection and Ranging (LiDAR) data. Tapirs travel and defecate more often in degraded forests, dispersing much more seeds in these areas [9,822 seeds per ha/yr (CI95% = 9,106; 11,838)] than in undisturbed forests [2,950 seeds per ha/yr (CI95% = 2,961; 3,771)]. By effectively dispersing seeds across disturbed forests, tapirs may contribute to natural forest regeneration – the cheapest and usually the most feasible way to achieve large-scale restoration of tropical forests. Through the dispersal of large-seeded species that eventually become large trees, such frugivores also contribute indirectly to maintaining forest carbon stocks. These functions may be critical in helping tropical countries to achieve their goals to maintain and restore biodiversity and its ecosystem services. Ultimately, preserving these animals along with their habitats may help in the process of natural recovery of degraded forests throughout the tropics.