Imperial expansion can have substantial impacts on the daily and long-term activities of colonized regions. However, statecraft can vary depending on local resilience and the decisions made by agropastoralists and other economic collectives. We explore how Wari expansion affected, and was affected by, pastoralists’ activities by examining the isotopic variation of camelid bone, teeth, and hair (or fibres) at three mid-valley (yunga) (500–2300 masl) sites in the Majes and Sihuas valleys of southern Peru. We report stable δ13C and δ15N isotopic compositions (n = 34) of keratin from previously published serial samples of camelid (Lama sp./Vicugna sp.) fibre from the site of Beringa in the Majes Valley, δ13C and δ15N values of bone collagen (n = 6) and δ13C values from tooth enamel bioapatite (n = 65) from Uraca in the Majes Valley, and δ13C and δ15N values of bone collagen (n = 30) from Quilcapampa in the Sihuas Valley. We compare diets between sites and between development phases of individual animals. Extensive networks of inter-valley trails connected neighboring yunga communities and camelid caravans enabled the exchange of goods and ideas. Stable isotope analysis of camelids from these three sites suggests that yunga communities in the Majes and Sihuas valleys were engaged in both highland and coastal camelid-caravan networks prior to Wari expansion that permitted local communities to maintain foddering flexibility. Herders maintained these networks into the Wari era, while also taking advantage of new trading opportunities as they became available.