The present study examines the prehistoric human skeletal remains retrieved starting from the 20s of the XX century in the deposit of the Farneto rock shelter, situated in the area of the ‘Parco dei Gessi Bolognesi e Calanchi dell’Abbadessa’ (San Lazzaro di Savena, Bologna, Northern Italy). An exact dating and a reliable interpretation of the assemblage had not been reached so far because of the lack of contextual data useful for dating purposes, the inaccurate recovery procedures of the remains, as well as their state of preservation. In fact, the skeletal remains from the Farneto rock shelter are highly fragmented and commingled, whereas reliable information about their original position and their recovery procedures are not available. Despite these difficulties, radiocarbon analyses allowed to clarify the precise dating of the remains, which date back to a final phase of the Neolithic and an early phase of the Eneolithic period in Northern Italy, testifying an early use of natural cavities for funerary purposes in the area. Moreover, the anthropological and taphonomic study of the skeletal remains shed light on the biological profile of the individuals and on some events that occurred after their death. In particular, the analysis of peri mortem lesions highlighted the existence of intentional interventions related to corpse treatment, referable to dismembering/disarticulation and scarnification, i.e., cleaning of bones from soft tissues. Finally, the comparison with other Neo/Eneolithic funerary contexts in Central and Northern Italy enabled a better understanding of these complex ritual practices.