Dual Dimensions in Regulating Nutritional Quality of Processed Soybeans: Genetic Basis and Processing Technology

• Food ingredients are fundamental to the nutritional quality of processed foods. • Processing technologies alter nutrient composition and bioavailability. • Natto is a nutritionally rich source of bioactive compounds. • Combining cultivars and processing methods can overcome product homogeneity. Soybeans have garnered significant attention as a vital source of nutrients due to the growing demand for functional foods and the persistent issue of hidden hunger. Herein, we employed multiple cultivars and processing, including soy beverage, fermented soy beverage, natto, and soy sprouts, to systematically evaluate the effects of cultivar and processing technologies on key bioactive components. Results demonstrated that the genetic background was the primary determinant of product nutritional quality. Consequently, high-folate/isoflavone cultivars retained significantly greater levels across all products. Processing exerted complementary effects: natto fermentation markedly increased tetrahydrofolate (up to 419%) and glycitein while degrading sucrose and forming melibiose. Liquid-based processing elevated β -glucoside isoflavones (e.g., daidzin +6.18-fold) but reduced malonylated forms (61.5–97.3%). Liquid-based processing and natto fermentation increased total folate content by 54.3% to 108% compared to raw soybean seeds. This study provides a scientific rationale for producing nutritionally enhanced soy foods through targeted cultivar selection and optimized processing.