The objective of this work was to carry out a preliminary study of the fractionation by supercritical CO2 (sc-CO2) extraction of two varieties of Peruvian beans (Phaseolus vulgaris L.), white (WB) and red (RB), to obtain two novel products: an oil rich in essential fatty acids and tocopherols and a defatted flour with high nutritional value and amino acids. The extraction temperature and pressure were optimized using the response surface methodology (RSM) and the extraction kinetics were optimized using the Spline equation. The results revealed that the best extraction conditions for WB and RB were 396.36 Bar, 40.46 °C, with an efficiency of 1.65%; and 391.995 Bar, 44.00 °C, with an efficiency of 1.12%, respectively. The WB and RB oils presented a high degree of polyunsaturation (63.2 and 52.8%, respectively), with oleic, linoleic, and linolenic fatty acids prevailing. Gamma-tocopherol was the predominant antioxidant in both oils. The residual flours (WB and RB) obtained after extraction with sc-CO2 had a high average content of proteins (23%), carbohydrates (61%), and minerals (3%). The limiting amino acids of WB were: Fen + Tyr, Leu, Lys, and in RB, only Leu was limiting. The viscosity of the solutions (20%) of the WB and RB flours mainly adjusted to the Waele’s Ostwald model (r = 0.988). It is concluded that both products (oil and bean flour) obtained in an optimized manner using an eco-friendly technology with sc-CO2 have high nutrient and bioactive component content and can be used in the development of new ingredients and healthy foods of plant origin.