Mortuary practices in southern Greece undergo a radical transformation at the beginning of the Mycenaean era (or Late Bronze Age, around 1700 BCE). This period sees the introduction of formal cemeteries, larger tombs, richer burials and a more complex ritual sequence involving multiple interments, tomb re-use and the ‘secondary treatment’ of earlier burials. ‘Secondary treatment’ is a rather vague, all-inclusive term, which includes various practices, such as disarticulating skeletons, mingling the bones and relocating them in piles or scatters either inside or outside the tomb (completely or selectively). Two questions arise: Why is this practice introduced? Why does it take different forms? The recent excavation of Ayios Vasilios North Cemetery in Laconia was designed on the basis of an integrated bioarchaeological strategy in order to provide the opportunity to fully explore these issues. While our ultimate goal is to understand the causes and consequences of the wider transformations in funerary practices, the focus of this paper is on one aspect: the re-use of graves and the secondary treatment of earlier burials. Through an integrated approach which aims to reconcile archaeological theory with current methodological advances in bioarchaeology and funerary taphonomy, we seek to reconstruct the funerary activities in great detail, in order to fully observe variation and change, and, ultimately, understand how this considerable variation may inform us on the re-definition of social relations at death, or shifting notions of the self. Beyond the specifics of the Mycenaean case-study, our aim is also to address broader methodological and theoretical questions, stressing the need for a true integration in the study of mortuary assemblages. To this end, we propose a taphonomy-oriented, methodological approach for the field recording and lab analysis of the human remains, drawing on current advances in archaeothanatology, forensic science, and analysis of commingled remains. This approach works best if placed within a clear theoretical framework, which recognises the manipulation of the dead body as closely associated with notions of personhood, and at the same time respects the historical specificity of the mortuary context and engages with the full complexity of contextual empirical data. Using the case of Ayios Vasilios in order to illustrate this process, our specific questions include: the formation characteristics of funerary assemblages, frequency and sequence of tomb use, diversity of secondary treatment, and age and sex differences in funerary treatment. Our results demonstrate a considerable extent of variation in funerary disposal and secondary treatment during this transitional period. Shifts of emphasis within this diverse treatment, especially regarding bodily fragmentation and modes of dispersal, suggest that, in Ayios Vasilios, a) age, but not sex, differences in funerary treatment were at play, b) mortuary transformation embodies the transformation from narrower (possibly household-based) associations to increasingly wider concepts of lineage and descent, c) tensions between tradition and innovation, as well as integration and differentiation, are evident in the variation of secondary treatment and co-existence of different forms (as already attested in other funerary and daily practices).