The analysis of subsistence practices in the Lesser Sunda Islands (from Bali in the west to Wetar and Timor to the east) provides data to interpret anatomically modern humans’ subsistence adaptation in insular environments. Most previous analyses of small vertebrate assemblages in these islands have focused on sites with evidence of intensive coastal subsistence, where the fish and other marine faunal remains can be assigned unequivocally to human predation. Inland sites, however, contain large quantities of murids, reptiles and bats of varying sizes, which could have been accumulated by different predators. Here we present the first detailed taphonomic analysis of the faunal assemblage recovered from the Pleistocene levels of the inland cave site Matja Kuru 2 (Timor-Leste), dominated by small murids, followed by large and giant murids, reptiles, birds, bats and fish bones. Through the study of skeletal representation, fragmentation and bone surface modifications in the large and giant murids, turtle and fish remains, we aim to determine whether humans were responsible for their presence in the older units of the site, whether they comprise natural deaths, or were prey of non-human predators such as raptors. Our analyses indicate differences in predator actions according to age of prey and taxa, with adult large and giant murids, freshwater turtles and fish showing evidence of human predation. The results presented here contribute significantly to understanding human behaviour in insular environments and deposition dynamics in karstic taphosystems in Island Southeast Asia, as well as providing a framework for future taphonomic studies in the region.