Some traditional zooarchaeological analyses assume that faunal assemblages associated with stone tools are basically the result of human behaviour. Under this view, in previous research of the Palaeolithic site of Amalda Cave, the site was defined as a fully anthropogenic assemblage. In this paper, new taphonomic analyses show a different interpretation, since in some cases, the associations of bones and stone tools are created and modified by more than one agent in a succession of events. In Amalda Cave, the high frequencies of tooth marks on some animal bones, in contrast to the marginal percentages of cut and percussion marks, as well as the fragmentation profiles, suggest that carnivores played a major role in the accumulation of small-sized animals. On the other hand, medium-sized and large-sized animals show high percentages of cut marks and other evidences of human behaviour in detriment of carnivore modification. The present review leads to the conclusion that carnivores were the main agent for the accumulation of small-sized animals, while hominids enjoyed a primary access to larger carcasses. This study underscores the crucial role of taphonomy to understand the zooarchaeological record of the Iberian Peninsula.