Due to increasing health consciousness, a lot of food supplements are sold and used. Dietary supplements of Glycine max (L.) MERR. are used as an alternative treatment for menopausal complaints such as hot flashes. Thereby, the effective soy compounds are the isoflavones daidzin, genistin, and glycitin. However, only the total soy extract content of the nutritional supplements is indicated. The aim of this study is to introduce a fast, efficient, and economic Fourier transformation infrared (FT-IR) spectroscopy method to quantify the active ingredients in the complex matrix of soy-based supplements. Five different nutritional supplements of Glycine max (L.) MERR. were purchased from a German pharmacy and were extracted with 80% aqueous methanol. A high-performance liquid chromatography (HPLC) method was used for the separation. The samples were concentrated and measured with infrared spectroscopy. An FT-IR method was established to quantify the active ingredients in the complex matrix of soy-based nutritional supplements. The partial least-squares algorithm was used to develop the method, which enabled the estimation of the content of particular isoflavones (daidzin R² = 0.86, glycitin R² = 0.94, genistin R² = 0.96) and the quantification of the total isoflavone content (R² = 0.92) despite peak overlap in the infrared (IR) spectra. The method for the quantification of the isoflavonol glycosides is precise with the standard error of prediction being 13.54%.