Several recent studies have demonstrated the complexity of funerary practices in megalithic burials. Mortuary taphonomy has proposed models to explain these practices, in which different actions, such as the generation of primary and secondary deposits, the selection and manipulation of bone remains, the extraction of materials from the grave, and so forth, can be identified. However, in the northern sub‐plateau of the Iberian Peninsula, the interpretation of funerary gestures related to megalithic tombs has not been systematically studied from the perspective of taphonomy. In this paper, we study two sites, Los Zumacales and La Lora, dated to the fourth millennium B.C. The analysis considers all the burial practices linked with megalithic tombs, with a focus on the social and natural processes involved in the formation of these complex mortuary deposits. In both examples, direct evidence of perimortem manipulation of human remains is documented by the presence of fresh fractures and cut marks in different long bones. As suggested in the discussion, this evidence may be related to secondary reduction practices following the initial deposition of the bodies.