Quinoa has been recognized as a complete food due to its balanced nutritional composition. Quinoa flour is used as an ingredient to improve the nutritional and functional characteristics of cereal-based foods. The physicochemical and functional (thermal and pasting) properties of flours and isolated starches of three Andean Peruvian quinoa varieties (Blanca de Hualhuas, BH; Rosada de Huancayo, RHY and Pasankalla, PK) were studied and the correlation among them properties were evaluated in order to explore their possible uses as a food ingredient. Proximal chemical composition of flour and isolated starches from quinoa varieties showed differences. Isolated starches from quinoa varieties showed a XRD Type A crystallinity patterns with polygonal shapes, small size, higher crystallinity degree and lower amylose content (<15%). The thermal (gelatinization temperatures and enthalpies) and pasting (temperature and time of gelatinization and viscosities) properties of flours and isolated starches showed differences and the principal component analysis demonstrated that those properties are significantly correlated to the starch and fat content. Based on the differences found among physicochemical and functional properties, isolated starch and flour of BH, RHY and PK quinoa varieties have potential as food ingredient for several cereal-based products.