Genistein and daidzein are well-known biologically active pharmaceutical compounds that play significant roles in the treatment of various diseases such as cardiovascular problems, cancer, etc. In some plants, the glycosides daidzin and genistin are present in ample amounts that can be converted into aglycones, daidzein and genistein, through hydrolysis. Here, magnetic cobalt ferrite alkyl sulfonic acid (CoFe₂O₄-Si-ASA) nanocatalyst was used for the hydrolysis of glycosides into aglycones. The application of CoFe₂O₄-Si-ASA nanocatalyst generated a maximum 8.91 g/L diadzein and 12.0 g/L genistein from 15.1 g/L daidzin and 19.3 g/L genistin with conversion efficiencies of 59.0% and 62.2%, respectively, from soybean glycosides at 80 °C in 3 h. The use of a modern nanocatalyst is preferred over enzymes because of its lower production cost, higher rate of reaction, higher stability, etc. To our knowledge, this is the first report on using nanocatalyst for the production of genistein and daidzein in a sustainable manner.