The goal of this study is to provide a taphonomic analysis of bone fragments found in harpy eagle nests in the Brazilian Amazonia, utilizing the largest sample of prey remains collected to date. Harpy eagle kill samples were collected from nine nests, between June 2016 and December 2020 in Mato Grosso, Brazil. We identified the specimens, calculated the number of identified specimens (NISP) and minimum number of individuals (MNI). These metrics were used to estimate bone survivability and fragmentation. A total of 1661 specimens (NISP) were collected, representing a minimum number of 234 individuals (MNI). We identified at least nine species of primates, which represent 63.8% of the individuals in the kill sample. Harpy eagles preyed mostly on the medium‐sized capuchin and bearded saki monkeys (28.2% of the MNI), and two‐toed sloths (17.7% of the MNI). The large woolly monkeys also represented a significant portion of the sample (11.5% of the MNI). Three distinct patterns of bone survivability were found, one characterizing two‐toed sloths, another characterizing medium‐sized monkeys, and a third typical of woolly monkeys. We conclude that harpy eagle predation leaves an identifiable signature on the prey with a bone survivability pattern specific to each taxon. The intertaxon variations observed in the taphonomic signatures of harpy eagle kills should be taken into account when evaluating the potential influence of these raptors as accumulators of bone material in both paleontological and neontological assemblages.