Quinoa has a high nutritional value, is based on protein content, oil, and phenolic compounds. The production of protein hydrolysates with antioxidant peptides has gained importance due to their properties against oxidation-related diseases and as an antioxidant in food, however, there is a lack of information on the operating costs of production on an industrial scale. In the present study, two technologies to extract the oil and separate the phenolic compounds prior to enzymatic hydrolysis were evaluated: (1) supercritical fluid extraction (SFE), using 35 g CO₂/min at 55 °C, 23 MPa and ethanol as cosolvent, and (2) Conventional solvent extraction (CSE) whit petroleum ether. The aim of this study was to compare the oil extraction yield, remaining phenolic compounds and quinoa protein hydrolysed (QPH) yield. Furthermore, an economic evaluation and sensitivity study was performed using SuperPro Designer 9.0 software, quinoa grain batches of 1.5 kg (laboratory) and 2500 kg (industrial scale) were considered. Oil extraction yield was 27.30% higher, remaining phenolic compounds was 0.4 times lower and QPH yield was 18.50% higher when using SFE compared to CSE. For both cases, the scale-up reduced the COM, the COM was lower in SFE compared to CSE, US$ 90.10/kg and US$ 109.29/kg, respectively and higher net present value (NPV), US$ 205,006,000 and US$ 28,159,000 compared to CSE. The sensitivity study considered the sale of by-products such as saponins and oil. The best scenario is when the sale of both by-products is included, the COM is reduced to US$ 28.90/kg (SFE) and US$ 57.06/kg (SCE), and profitability also improves. In addition, the significance the COM and NPV was statistically evaluated, there are no significant differences on an industrial scale. Both processes are economically promising, especially when the QPH and by-products are produced in large scale and sold at the current market price.