This study aimed to valorize Sacha Inchi cake—a byproduct of oil extraction—through the development of a methodology to produce a gluten free, high-protein flour with enhanced nutritional properties. Owing to its rich protein content, Sacha Inchi cake represents a promising alternative to conventional wheat; however, its inherent saponin content demand the implementation of targeted removal strategies. Two desaponification approaches were assessed: a thermal extrusion treatment, varying barrel temperature (80–90 ℃ and 100–110 ℃) and nozzle diameter (8, 12 and 15 mm); and a hydrothermal treatment, conducted at (30, 45 and 60 ℃) for (1, 2 and 3 h). Thermal extrusion failed to reduce saponins below the established safety threshold (0.1%). In contrast, hydrothermal processing at 60 ℃ for 2 h and 3 h achieved saponin reductions of 98.63% and 99.67%, respectively. Both treatments improved the protein profile of the resultant flours, and all processed samples were confirmed gluten free. These findings demonstrate that hydrothermal treatment is an effective, low energy strategy for transforming Sacha Inchi cake into a high value functional ingredient suitable for novel food formulations and the promotion of circular economy principles in agro industry.