Vegetable oils are rich in health-beneficial compounds, including fatty acids, phenolic compounds, natural antioxidants, and fat-soluble vitamins. However, oil extraction methods can influence their composition. This study aims to understand the chemical basis for developing a green process to extract oils from two Andean seeds, cañihua (Chenopodium pallidicaule) and tarwi (Lupinus mutabilis). Ethanol, considered a green solvent, is compared to petroleum ether used at the laboratory level and hexane used at the industrial scale for extracting oils. The extraction efficiency is assessed in terms of yield, fatty acids profile, polar and neutral lipids, tocopherols, phenolic compounds, and antioxidant capacity. The chemical composition of edible commercial oils, such as sunflower, rapeseed, and olive oils, was used as a reference. Hexane had the highest extraction yield, followed by petroleum ether and ethanol. However, the oils extracted with ethanol having yields of tarwi 15.5% and cañihua 5.8%, w/w showed the significatively superior content of tocopherols (α, γ, and δ); phenolic compounds; and antioxidant capacity. In addition, ethanol-extracted (EE) oils have higher levels of polar lipids, such as phosphatidylcholine and phosphatidylinositol, than those extracted with the other solvents. Remarkably, EE oils presented comparable or slightly higher levels of monounsaturated fatty acids than those extracted with hexane. Finally, compared to the commercial oils, tarwi and cañihua EE oils showed lower but acceptable levels of oleic, linoleic and palmitic acids and a wider variety of fatty acids (10 and 13, respectively). The composition of tarwi and cañahua oils extracted with ethanol includes compounds associated with nutritional and health benefits, providing a sustainable alternative for oil production.