A method for producing a composition containing soluble isoflavones is described, which uses soybean materials as raw materials. The composition is obtained in a natural state without addition of solubilizing agents and chemical modification, and has high solubility under neutral to acidic conditions and good long-term stability under refrigeration. By removing the insoluble materials from the water-extract liquid of a soybean material having a pH value of 2-7 and a temperature of 0-17° C., a composition containing isoflavones can be efficiently obtained with high solubility under neutral to acidic conditions and good stability under refrigeration.