A physiologically active substance of aglycon type, in particular, aglycon isoflavone, can be efficiently produced, without resort to any acid/alkali treatment or fermentation and substantially without changing the physical properties of a material, by treating the material with a sufficient amount of diglycosidase for a sufficient period of time at an appropriate temperature and pH so that a physiologically active substance of glycoside type contained in the material can be converted into the physiologically active substance of aglycon type. Moreover, by using diglycosidase and/or a specific enzyme preparation, the aglycon content in a protein or protein-containing food can be increased and the flavor thereof can be improved.