White quinoa protein isolates (WQPI), red quinoa protein isolates (RQPI) and black quinoa protein isolates (BQPI) were isolated and extracted from white, red and black quinoa, respectively, after degreasing with n-hexane, alkaline dissolution with NaOH and precipitation with hydrochloric acid. The effects of pH (2.0~10.0) and NaCl concentration (0~0.6 mol/L) on the physicochemical properties and functional characteristics of WQPI, RQPI and BQPI were evaluated through polyacrylamide gel electrophoresis, Zeta potential and particle size determination, as well as surface hydrophobicity, protein solubility, water-holding capacity, oil-holding capacity, emulsifying activity, foaming property and gelation property tests. The results showed that the main components of WQPI, RQPI and BQPI were all 11S globulin and 7S globulin cross-linked via acidic subunits and basic subunits through disulfide bonds, but with significant difference in their contents. The average particle size and surface charge of the three proteins were highly dependent on pH, and their surface hydrophobicity significantly decreased as pH increased. The pH far from the isoelectric point (about 5.0) could significantly improve the solubility, emulsification and foaming property of the protein, but reduce the stability of the foam. Under neutral conditions, WQPI and RQPI exhibited better gelation and interfacial properties than BQPI. The influence of NaCl on the solubility, emulsification and foaming properties of proteins was correlated to its concentration. The gelation properties of WQPI and RQPI were significantly better than those of BQPI. The gel structures formed by WQPI and RQPI with a mass concentration of 120 g/L were complete and had good standing properties, while only BQPI with a mass concentration of 180 g/L could form a gel with standing properties.