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Quinoa (<i>Chenopodium quinoa</i> Willd.) has recently received increasing interest from both scientists and consumers due to its suitability in gluten-free diets, its sustainability, and its claimed superfood qualities. The aim of this paper is to systematically review up-to-date studies on quinoa functional components and anti-nutritional factors, in order to define a baseline for food scientists approaching the investigation of quinoa phytochemicals and providing evidence for the identification of healthier sustainable foods. State of the art evaluations of phytochemical contents in quinoa seeds were obtained. It emerged that phenolic compounds are the most investigated functional components, and spectrophotometric methods have been mostly applied, despite the fact that they do not provide information about single components. Saponins are the most studied among anti-nutritional factors. Betalains, tannins, and phytoecdysteroids have been poorly explored. Information on factors affecting the phytochemical content at harvesting, such as quinoa ecotypes, crop geographical location and growing conditions, are not always available. A comprehensive characterization, encompassing several classes of functional components and anti-nutritional factors, is mainly available for quinoa varieties from South America. However, defining a standard of quality for quinoa seeds is still challenging and requires a harmonization of the analytical approaches, among others.