The archaeology of the pre-contact Andes provides an ideal study of human responses to climate change given the region's extreme climatic variability, excellent archaeological preservation, and robust paleoclimate records. We evaluate the effects of climate change on the frequency of interpersonal violence in the south-central Andes from ca. 1.5–0.5 ka (AD 470–1540) by comparing incidents of skeletal trauma observed among 2753 crania from 58 sites to rates of ice accumulation at the Quelccaya Glacier. We find that, in the highlands, the odds of identifying inter-personal violence increase on average by a multiplicative factor of 2.4 (1.8–3.2; 95% C.I.) for every 10-centimeter decrease in annual ice accumulation. Our statistical analysis does not detect a relationship between ice accumulation and interpersonal violence rates among coastal or mid-elevation populations. This disparity likely resulted from variable economic and sociopolitical strategies at different elevations. The failure of rain-fed agriculture during periods of drought and concomitant dissolution of organizing polities likely predisposed highland populations to socioeconomic stress and violent competition for limited resources. Conversely, diversity among lowland and midland economies may have buffered against the effect of drought.