Objectives Inca imperial strategies of political and territorial expansion varied across conquered regions depending on local ecology and cultural resistance, and Chachapoya peoples in Peru's forested northeastern Andes were renowned for their rebellions against the invaders. The cliff tombs of Los Pinchudos (AD 1470–1535) present opportunities to use stable isotopes to: (1) explore dietary and mobility patterns from a mortuary community interred at a site attributed to the poorly‐known Chachapoya culture during the period of Inca domination, and (2) explore the origins of the individuals as either local or foreign (Inca). Using biochemical tracers, we can help resolve the impact of foreign influence and changes in population and social structure during imperial occupation. Materials and Methods While it is difficult to reconstruct individual life histories from incomplete skeletons, stable isotopic analysis of multiple skeletal tissues provides a direct means of characterizing diet and residential mobility. Values of stable carbon (δ13C), nitrogen (δ15N), and oxygen isotope (δ18O) ratios were determined in bone and dentine collagen and bone and enamel carbonate from 28 samples (11 paired tissues) from males, females, and juveniles from Los Pinchudos. Results Dietary signatures are consistent with a mixed but more C3‐based plant and protein‐based diet with moderate proportions of terrestrial animals. Oxygen isotopic values demonstrate limited variation between paired tissues, with a few possible nonlocal individuals buried in one particular tomb at the site. Compared to other Andean areas that underwent imperial domination, these data do not demonstrate expected dietary shifts. Discussion These are the first isotopic data from a Chachapoya site and our research shows evidence for minimal non‐local presence in this commingled burial assemblage. The regional diet reconstructed at Los Pinchudos (2850 masl) focused on resources of higher altitude tuber crops, beans, and grains (C3) and terrestrial protein rather than on lower elevation grasses such as maize (C4) as in other highland Andean regions under Inca control. During imperial domination, inhabitants of this region appropriated Inca materials goods but continued to construct tombs in the local manner even though a potentially diverse population was occupying them.