It is intended to easily separate saponins from isoflavones extracted from starting soybeans thereby giving highly pure saponins at a high yield on an industrial scale. Saponins can be highly efficiently separated from isoflavones by performing multistage extraction under mild conditions such that malonyl isoflavone glycoside, from among isoflavones contained in the starting soybeans, is not converted into isoflavone glycoside, acetyl isoflavone glycoside or isoflavone aglycon. Thus, highly pure saponins can be obtained at a high yield on an industrial scale.