Genomic, archaeological, historical, and biogeochemical data are integrated to examine the genomes of six individuals from two cemeteries in the Chincha Valley of southern Peru. Results demonstrate consistency among these independent datasets in support of a model of north Peruvian coast peoples moving to the Chincha Valley during the Late Horizon (1400 – 1532 CE). Our transdisciplinary work provides strong support for Inca resettlement, a state policy that reshaped the Andean sociopolitical landscape yet represents one of the most notoriously difficult phenomena to identify in the archaeological record. This research offers an ideal case study that sets a methodological standard for investigating ancient mobility in complex societies by synthesizing aDNA with multiple independent lines of evidence.