We present a food quality evaluation of Zea mays L. amylacea from Lluta Valley, northern Chile, a species with important nutritional qualities for historic and current populations in the area. Studies were made of proximal analyses, antioxidant activity, and characterization of the fatty acids fraction. Also, the fatty acids fraction of six ancient maize samples were studied, searching for possible archaeometric markers. The results of the proximal analysis show that the modern Lluteno maize has a high carbohydrates and protein content, low moisture, high ash residue and low antioxidant activity (free radical scavenging). The oleic and linoleic fatty acids show the highest concentrations in Lluteno maize. The presence of omega-6 and omega-9 present in the maize could provide health benefits against diseases such as type II diabetes and cardiovascular diseases. Finally, the fatty acid distribution of the ancient maize samples cluster in two categories, one of which was similar to the modern Lluteno maize. Thus, the fatty acid fraction can be considered in the future to investigate the antiquity and evolution of Lluteno maize, and his influence on the health of the local populations.