We examined stable isotopes (δ13C, δ15N, and δ34S) of camelid, cavid, and cervid remains from Upanca, an archaeological site located in the Southern Nasca Region on the south coast of Peru. Occupation at the site began in the Middle Archaic (around 3200–3000 BC) and continued through the Nasca period (AD 100–650). Remains predating 2500 BC show low δ13C and δ15N values, whereas remains after this time show increasing and especially more variable isotopic values. We interpret this pattern as marking both a process of agricultural intensification and camelid husbandry diversification. Agricultural intensification began first with C3 plants in fertilized fields, beginning around 2200 cal BC, followed by an increasing use of C4 plants (maize, kiwicha, or both), particularly after 800 cal BC. By the beginning of the first millennium, people were using a diverse range of strategies to raise llamas and alpacas, including feeding them wild or cultivated C3 plants, feeding them cultivated C4 plant foods, mixing C3 and C4 plant foods, foddering some in natural coastal environments, and acquiring still other camelids by hunting wild stocks (guanaco, vicuña). Data also suggest that cavids were consuming at least some C4 products after 1000 cal BC and that the use of C4 plants increased over time.