The effect of two pretreatments on the antioxidant activity was evaluated in quinoa protein hydrolysate, using supercritical CO2 extraction and ethanol as cosolvent, this type of pretreatment was compared to a conventional petroleum ether extraction method without recovery of bioactive compounds. The extractions were carried out at a temperature of 55°C and a pressure of 23 MPa using ethanol (7–8 g quinoa/100 ml); the CO2 mass flow was 35 g/min, the extraction time was 240 min and the particle size was 500 µm, enzyme COROLASE® 7089 was applied for enzymatic hydrolysis, finally ABTS test assessed antioxidant activity. A significant effect was found on the degree of hydrolysis (23.93%) and antioxidant activity (1,181.64 μmol TE/g protein) compared to a conventional method (24.33%) and (1,448.84 μmol TE/g protein). In conclusion, our results suggest that the use of supercritical CO2 and the addition of ethanol as cosolvent are the interesting green technology, to recovery oil and separate phenolic compounds prior to enzymatic hydrolysis to avoid interference with biological activities from quinoa protein hydrolysates, and shows highest antioxidant activity to be incorporate in food products.