The amino acid composition and the physicochemical and functional properties of quinoa protein isolates were evaluated. Protein isolates were prepared from quinoa seed by alkaline solubilization (at pH 9, called Q9, and at pH 11, called Q11) followed by isoelectric precipitation and spray drying. Q9 and Q11 had high levels of essential amino acids, with high levels of lysine. Both isolates showed similar patterns in native/SDS-PAGE and SEM. The pH effect on fluorescence measurements showed decreasing fluorescence intensity and a shift in the maximum of emission of both isolates. Q9 showed an endotherm with a denaturation temperature of 98.1 degrees C and a denaturation enthalpy of 12.7 J/g, while Q11 showed no endotherm. The protein solubility of Q11 was lower than that of Q9 at pH above 5.0 but similar at the pH range 3.0-4.0. The water holding capacity (WHC) was similar in both isolates and was not affected by pH. The water imbibing capacity (WIC) was double for Q11 (3.5 mL of water/g isolate). Analysis of DSC, fluorescence, and solubility data suggests that there is apparently denaturation due to pH. Some differences were found that could be attributed to the extreme pH treatments in protein isolates and the nature of quinoa proteins. Q9 and Q11 can be used as a valuable source of nutrition for infants and children. Q9 may be used as an ingredient in nutritive beverages, and Q11 may be used as an ingredient in sauces, sausages, and soups.