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Soybeans are commonly known as a valuable source of biologically active compounds including isoflavones as well as allantoin and alpha-hydroxy acids. Since these compounds exhibit skin therapeutic effects, they are widely used in the cosmetic and pharmaceutical industries. The presented paper shows the optimization of three solvent systems (ethanol, water, and 1,3-propanediol) to increase the extraction efficiency of isoflavones (daidzin, genistin, 6″-O-malonyldaidzin, 6″-O-malonylglycitin, 6″-O-malonylgenistin), allantoin, and alpha-hydroxy acids (citric acid, malic acid) from soybean leaves. A simplex centroid mixture design for three solvents with interior points was applied for the experimental plan creation. Based on the obtained results of metabolite extraction yield in relation to solvent composition, polynomial regression models were developed. All models were significant, with predicted R-squared values between 0.77 and 0.99, while in all cases the model’s lack of fit was not significant. The optimal mixture composition enabling the maximization of extraction efficiency was as follows: 32.9% ethanol, 53.9% water, and 13.3% propanediol (v/v/v). Such a mixture composition provided the extraction of 99%, 91%, 100%, 92%, 99%, 70%, 92%, and 69% of daidzin, genistin, 6″-O-malonyldaidzin, 6″-O-malonylglycitin, 6″-O-malonylgenistin, allantoin, citric acid, and malic acid, respectively. The solvent mixture composition developed provides a good extraction efficiency of the metabolites from soybean leaves and high antioxidant properties.