At high altitude, the drop in atmospheric pressure limits cellular oxygen supply (hypoxia), challenging cellular homeostasis. Despite the chronic hypoxic stress, human populations have resided above 3000m for thousands of years. Over hundreds of generations, natural selection of multiple gene regions underpinning putatively adaptive physiological traits has occurred. Signals of positive selection have been identified within genes that are master metabolic regulators, including the hypoxic inducible factor (HIF) system. However, yet little is known of how these adaptive genetic signals affect metabolic function. Here, links are presented between genomic selection signals within EPAS1, encoding HIF-2α, and systemic and cellular metabolic phenotypes in two distinct highland populations: the Himalayan Sherpa and Andeans. In a cohort of 61 Sherpa’s (34 female), associations were detected between a putatively adaptive haplotype within EPAS1 and systemic metabolite abundance at Everest Base Camp (5300m). Subjects carrying the adaptive EPAS1 haplotype displayed lower abundance of triglycerides (46-54 carbons), diglycerides, valine, leucine and tyrosine, indicating adaptive alterations to both lipid and amino acid metabolism in Sherpas. In Andeans, a novel single nucleotide variant in EPAS1 (rs570553380) identified from 40 Quechuan subjects residing in Cerro de Pasco, Peru (4340m)¹, was incorporated into human embryonic kidney cells using precision genome editing. Following 24 hrs hypoxia (1% O₂), we demonstrate altered expression of specific HIF targets and suppression of mitochondrial O₂ consumption rates in normoxia, which was sustained in hypoxia. This occurred with no change in growth rate or viability and no compensatory increase in glycolytic capacity, indicating downstream mechanisms that may prime cells for hypoxic exposure by preserving mitochondrial O₂ consumption in Andeans. Together, this work indicates metabolic mechanisms downstream of genetic variance in the HIF system are crucial for adaptation to hypoxia in both Sherpa and Andean highlander populations.