Abstract: A method is provided for separating and recovering protein and isoflavones from a plant material. A clarified protein extract of the plant material is prepared and contacted with a polar ion exchange resin, such as an anion exchange resin allowing the isoflavones in the extract to bind with the ion exchange resin and depleting the extract of isoflavones. A protein extract which has been depleted of isoflavones is separated from the ion exchange resin, and an isoflavone depleted protein material is recovered from the isoflavone depleted extract. After removal of the isoflavone depleted extract from the resin, the isoflavones are separated and recovered from the ion exchange resin. Recovered isoflavone glycosides and isoflavone glycoside conjugates may be converted to their corresponding aglucone isoflavone form.