Taphonomic modifications to Neolithic human skeletal remains from six rock-cut tombs in Malta has provided key information about funerary practices and the local environment. Application of microscopic analysis, computed tomography (CT) scanning, and 3D imaging of the modifications has allowed their comparison with similar examples in modern and archaeological skeletal material. The modifications are interpreted as pupal chambers and feeding damage by dermestid beetles. Based on observation of the behaviour and ecology of dermestid beetles, we suggest several scenarios for funerary practices at the Xemxija tombs which nuance our current understanding of collective burial during the late Neolithic in Malta.