The physicochemical characteristics of soluble nano-sized quinoa protein isolates prepared by combined pH shifting and high-pressure homogenization were studied. Commercial quinoa protein isolates were exposed to pH shifting at acidic (pH 2-6) or alkaline (pH 8-12) conditions followed by high-pressure homogenization earlier than neutralizing of pH to 7.0. The pH method under pH 12 followed by high-pressure homogenization was found as the most efficient treatment in the reduction of protein aggregate sizes and transparency, improving soluble protein content and surface hydrophobicity. Quinoa protein isolates treated with pH 12 and high-pressure homogenization increased the solubility from 7.85% to 78.97%, creating quinoa protein isolate nanoaggregates with an average size around 54 nm. The quinoa isolate aggregates were used to produce oil-in-water nanoemulsions, which demonstrated the good stability for 14 d at 4 °C. This new approach might present an effective technique for the modification of functional features of quinoa protein isolates.