This work presents the results from the excavation of a multiple burial in a pseudo-tumular structure constructed in the Cueva Mayor cave in the Sierra de Atapuerca (Burgos), specifically focusing on the entrance of this cave in an area known as El Portalón archaeological site. We recovered the skeletal remains of a minimum of eight individuals from several altered primary burials with bones showing different levels of associated grave goods and faunal remains. A series of radiocarbon dates obtained from seeds, human and animal bones, place these burials at the end of the fifth millennium BP. The domestic animals and ceramics suggest a complex and symbolic human–animal relationship. The information obtained from the site of El Portalón significantly broadens our understanding of funerary rituals during the Chalcolithic period.