Undernutrition and overnutrition are interconnected. Yet few studies have examined the "double burden of malnutrition" (DBM) over time in indigenous communities. We investigated changes in the food systems and nutritional health of Awajún communities in the Peruvian Amazon in the 1970s and in 2013. Methods included ethnography, 24 hr food recalls, and biological measures. In 2013, the number of traditional foods consumed decreased to 10% of levels in the 1970s and the number of market foods consumed increased 40-fold. Rates of anemia and obesity were also substantially higher in 2013 compared to the 1970s (23% vs 6% for anemia and 30% vs. 0% for obesity) indicating a DBM has emerged. Examining the predictors of hemoglobin levels and body mass indices in the 2013 sample reveals that this DBM is differentially impacting women and that risk for obesity among the Awajún is associated with multiple proxies of market integration beyond just the consumption of market foods. These findings highlight the complex pathways by which rapid lifestyle changes are creating gendered health inequalities within indigenous communities over time