The combined effects of extrusion and enzymatic hydrolysis with a neutral protease (endoprotease) on quinoa germ flour have been studied in this work. A 2 × 3 factorial design with two temperature levels (60 °C - 90 °C - 100 °C and 60 °C - 100 °C - 120 °C) and three protease concentrations (0 %w/v, 0.6 %w/v, 1.2 %w/v). The hydrolyzed quinoa germ flours were characterized in terms of their physicochemical and rheological properties, antioxidant capacity by ABTS+, in-vitro digestibility of carbohydrates and protein, infrared spectroscopy, and their rheological behavior in aqueous dispersion at 12 % (w/w). The results showed that enzymatic hydrolysis and extrusion temperature influenced hydrolyzed quinoa germ flours properties. The highest protein digestion (65 mg leucine/g protein) was obtained with 0.6 % protease and 100 °C extrusion. Antioxidant activity increased with protease concentration but decreased with temperature. The solubility of hydrolyzed quinoa germ flours improved after enzymatic hydrolysis, while water absorption decreased. The treatment with 0.6 % protease and 100 °C extrusion produced high amounts of slowly digestible starch and RS, and enhanced protein digestibility compared to the other treatments. Infrared spectroscopy revealed changes in amide functional groups A, B, and I due to hydrolysis. The modification of these flours through enzymatic hydrolysis and extrusion after the tecno-functional properties. This research highlights the importance of understanding the interactions between different sources of proteins and how they contribute to the overall characteristics of the final product.