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The unraveling of the Wari Empire circa AD 1000 is marked by violent political upheaval and climate change. Such social, economic, and environmental disruptions are often accompanied by significant shifts in human diet and mobility in affected populations. We examine diachronic change through isotopic analysis of human remains from an early burial site (Turpo; AD 880-990) and three later sites (Cachi, Ranracancha, and Pucullu; similar to AD 1100-1260), all from the Apurimac highlands of south central Peru. Carbon, oxygen, and strontium from tooth enamel are used to explore changes in diet and mobility in 43 sampled individuals. Due to the tumultuous transition and increased violence that occurred as Wari influence waned, we expect to see visible shifts in dietary and mobility patterns between individuals sampled from earlier and later sites. Specifically, we hypothesized that populations at later sites would exhibit a wider dietary spread, a more circumscribed use of water, and an increased degree of mobility as mechanisms for dealing with changing social, political, and environmental factors. These changes would also be reflected in individual isotope profiles, with the hypothesized changes at the later sites revealed through increased standard deviation of carbon isotope values, decreased standard deviation of oxygen isotope values, and the presence of outlier strontium isotope values, as compared with the values from the earlier site. Results support the argument that human diet and movement were affected by the political, social, and environmental upheavals that marked this key transition period in Andean history from the Middle Horizon (similar to AD 600-1000) to the Late Intermediate Period (similar to AD 1000-1450).