The objectives of this work were to investigate the nutritional and physicochemical characteristics as well as the functional properties of quinoa protein isolates (QPI) from different varieties, and to determine their potential use of such protein isolates in food products. Proteins were isolated by isoelectric precipitation at pH 5 from quinoa flour, and the QPI had a protein percentage of over 85%. The comparison of the flours and QPI electrophoretic profiles indicated that the extraction method allowed isolating practically all proteins of each variety. All the varieties analyzed had high lysine content, compared with cereals, and the essential amino acid content of Bolivian varieties was higher than varieties from Peru. The pH value affected the solubility and foaming capacity, and the magnitude of effects depended on the variety. Cluster analysis showed a strong influence of variety source and amino acid composition on protein physicochemical and functional properties; samples from Bolivia (cluster 2) were characterized as having the highest thermal stability, oil binding capacity, and water binding capacity at acid pH; samples from Peru (cluster 1) had the highest water binding capacity at basic pH and foaming capacity at pH 5. QPI presented a potential as an alternative vegetable protein for food application, in particular for vegetarian and vegan diets.