Abstract Natural and anthropogenic taphonomic processes in seated-flexed human burials introduce variability in the archaeological record that may obscure evidence for standardization of funerary practice and prolonged ritual interaction with ancestral remains. This archaeothanatological study of 182 seated-flexed burials from a Tiwanaku-affiliated site in southern Peru (500–1100 CE) examines evidence for primary burial, post-depositional decomposition and dissociation, sediment infilling, and disturbance caused by human agents. The results suggest a high degree of standardization in body preparation, and a protracted timeline for Tiwanaku funerary rituals that included secondary manipulation of human remains. Although archaeothanatological studies of seated-flexed burials are rare in the Andes and elsewhere, this study calls attention to the importance of collecting data from various lines of evidence to disentangle natural and anthropogenic taphonomic processes in this popular form of burial.