The rock‐cut tomb of Bolores in the Portuguese Estremadura dates primarily to the Late Neolithic/Copper Age (2800–2600 BC) and, in a series of recent excavations, has yielded thousands of fragmented, commingled human bone specimens. The primary goals of the present study were to determine the minimum number of individuals interred in the tomb and to analyse spatial patterns in fragmentation intensity to identify natural and anthropogenic taphonomic processes. To investigate these research questions, the authors employed a simplified version of an established method in zooarchaeology to the study of human remains. Human bone specimens were recorded by the presence of osteological landmarks rather than the zones used in similar studies. This recording system allowed for calculation of the minimum number of individuals (further refined through dental analysis) and generated the NISPs (Numbers of Identified Specimens), minimum number of elements, fragment counts and landmarks sums essential to the conjoining and fragmentation studies. Fragmentation analysis led to the identification of four possible use areas in the tomb: two for primary inhumations and two for secondary deposits created by cleaning out the burial chambers at Bolores. We found that the application of multiple zooarchaeological methods to the study of commingled human remains has the potential to provide a more fine‐grained understanding of site biography and taphonomy than human osteological methods alone. Copyright © 2015 John Wiley & Sons, Ltd.