All over the world, there are species which may be considered as neglected or underutilized despite their nutritious properties. At present, such crops contribute to food security in isolated areas by providing energy and nutrients in a diversified diet. Such genetic heritage—improved by ancient cultures—is under threat of losing biodiversity as well as the traditional knowledge associated with their cultivation and usage. Among these species, the Andean root and tuber crops (ARTCs) constitute a valuable resource which should be preserved and popularized because of their food and functional properties. We studied three ARTC species (mashua, arracacha, and yacon) to provide data on their composition, essential for increasing their use globally. We compared their nutritional values with the values of more widely used crops. Important differences in nutrient composition among ARTC landraces were found. Mineral nutrients showed significant differences among species. Considerable variations in the contents of prebiotics like fructooligosaccharides or functional elements (antioxidants and glucosinolates) were found among species and intraspecific samples. Certainly, these species are important assets to complement human nutrition and to secure supply of functional elements for healthy diets.