Quinoa ( Chenopodium quinoa Willd.) is a grain of great nutritional interest that gained international importance during the last decade. Before its consumption, this grain goes through many processes that can alter its nutritional value. Here we report the effect of processing (polishing and milling) and cooking (boiling and steaming) on the saponin content, mineral profile of 14 elements using Inductively Coupled Plasma-Optical Emission Spectrometry (ICP-OES), protein content, and total phenolic compound. The polishing caused an average drop in the saponin content from 1.7% to 0.46% but induced important losses in mineral content (K, Mg, Ca, Zn, Co, Cu, Fe, Mn, and Ni), and phenolic compounds. However, the greatest nutritional degradation happened after milling due to the elimination of seed teguments and embryos, where over 50% of many minerals, 60% of protein content, and almost the totality of phenolic compounds, were lost. Cooking effect was less important than processing, but some significant losses were attested. Boiling caused a loss of up to 40% for some minerals like K, B, and Mo because of their hydrosolubility, and 88% of the polyphenols, while steaming allowed a better retention of those nutrients. Consuming polished quinoa instead of semolina and using steaming instead of boiling are trade-offs consumer needs to make to get optimal benefits from quinoa virtues.