Quinoa (Chenopodium quinoa Willd.) and kañiwa (Chenopodium pallidicaule) are very nutritious crops native to the Andean region of South America. Both grains contain good-quality proteins and micronutrients such as iron, calcium and vitamins. Their fat content is relatively high, making them a source of essential fatty acids and tocopherols. Kañiwa has a particularly high dietary fibre content, thus being beneficial for human health. Quinoa and kañiwa seeds are major sources of flavonoids which consist mainly of glycosides of the flavonols kaempferol and quercetin. Processing Andean grains can lead to changes in the content of beneficial bioactive compounds; precautions must thus be taken to avoid losses. The traditional way to process Andean grains is cooking and roasting. It has been reported that it is possible to maintain the level of phenolic compounds in quinoa after cooking, if the cooking water is not discarded. Heat treatments can cause the release of phenolic compounds from the grain matrix, making them more bioavailable. During the milling of Andean grains, the bran fraction should be collected and used in food products because the majority of bioactive compounds are concentrated in this fraction.