Apex predators typically affect the distribution of key soil and vegetation nutrients through the heterogeneous deposition of prey carcasses and excreta, leading to a nutrient concentration in a hotspot. The exact role of central-place foragers, such as tropical raptors, in nutrient deposition and cycling, is not yet known. We investigated whether harpy eagles (Harpia harpyja) in Amazonian Forests—a typically low soil fertility ecosystem—affect soil nutrient profiles and the phytochemistry around their nest-trees through cumulative deposition of prey carcasses and excreta. Nest-trees occurred at densities of 1.5–5.0/100 km2, and each nest received ~ 102.3 kg of undressed carcasses each year. Effects of nests were surprisingly negative over local soil nutrient profiles, with soils underneath nest-trees showing reductions in nutrients compared with controls. Conversely, canopy tree leaves around nests showed significant 99%, 154% and 50% increases in nitrogen, phosphorus and potassium, respectively. Harpy eagles have experienced a 41% decline in their range, and many raptor species are becoming locally extirpated. These are general examples of disruption in biogeochemical cycles and nutrient heterogeneity caused by population declines in a central-place apex predator. This form of carrion deposition is by no means an exception since several large raptors have similar habits.