Background: Currently, the consumption of high-protein foods that replace animal sources is increasing, a trend that promotes the design of new food systems. Spectroscopy methods with physicochemical tests allow for rapid and reliable identification of macronutrients and bioactive compounds. Methods: Snacks were made using hyperproteic quinoa flour (HPQF) and sacha inchi flour (SIF) through an extrusion process and subsequent compression molding. Spectra infrared (IR) analysis was used to identify macronutrients such as starch, proteins, lipids, and fiber. Specific frequencies were selected that provided the greatest discrimination of the sample. Physicochemical measurements were performed using extractable (EPC) and hydrolyzable (HPC) phenolic compound analyses, carotenoid content, and antioxidant capacity through ABTS• + (2,2-azinobis- 3-ethylbenzothiazoline-6-sulphonic acid), DPPH (2,2-diphenyl-1-picrylhydrazyl), and FRAP (ferric reducing antioxidant power) methods. Color and texture parameters of the snacks were also measured. Results: The identification of macronutrients using Fourier transform infrared spectroscopy – attenuated total reflectance (FTIR–ATR) was as follows: lipids showed two characteristic peaks at 2870 and 2960 cm−1; protein showed three peaks at 1540, 1630, and 1660 cm −1; starch showed two peaks at 1170 and 1155 cm −1. Regarding the content of free polyphenols, hydrolyzable polyphenols and carotenoids, the mixtures added with the highest inclusion of quinoa, i.e. 50%, showed the highest values of 3.05 mg GAE/g, 14.16 mg GAE/g and 14.06 µg-β carotene/g of dry base sample, respectively. The snacks showed significant differences (p<0.05) in the antioxidant properties determined by the ABTS and FRAP methods, with the highest values in the samples with 50% HPQF. The inclusion of HPQF was associated with a higher browning index, and snacks with a higher quinoa content exhibited greater hardness and crispness. Conclusions: Snacks were obtained with protein percentages between 26–33%, containing bioactive compounds, gluten-free, and without the addition of oil during their production.