This study presents a diachronic analysis of pathological conditions from two samples of human remains at the archaeological site of Tumilaca la Chimba, Peru. The site includes two occupations, one dating to the terminal Middle Horizon or early Late Intermediate Period (LIP; ca. 950–1250 CE), as the Tiwanaku state underwent collapse. Despite political fragmentation, this occupation is characterised by substantial cultural continuity in Tiwanaku practices. The second occupation dates to the later LIP (ca. 1250–1476 CE) and is associated with significant changes in material culture. This study analyses skeletal data derived from cemeteries associated with each occupation in order to compare proxies of nutritional status, infection, and trauma. Paleopathological analysis of individuals from the terminal Middle Horizon Tumilaca cemeteries (N = 20) and LIP Estuquiña cemetery (N = 23) reveals significant differences in age and sex distributions; this could be an artefact of looting and differential excavation or a possible shift in fertility and population demography. There are also differences, though not statistically significant, in the frequencies of pathological conditions including cribra orbitalia, which is higher in the Tumilaca sample, and oral decay, which is higher in the Estuquiña sample. These results tentatively suggest that physiological stressors—particularly those occurring in childhood—did not necessarily abate at this site over time but rather shifted in their causes. These results underscore the importance of bioarchaeological contributions to theorising local experiences of larger sociopolitical transitions in the pre‐Hispanic Andes.