A soy protein isolate that has increased amounts of isoflavones and saponins and a high Nitrogen Solubility Index ("NSI") is produced by a process that involves ultrafiltration and the avoidance of isoelectric precipitation. The soy protein isolate has at least about 90.0 wt. % protein of total dry matter; an isoflavone content of at least about 1.0 mg/g isoflavones of total dry matter; a Nitrogen Solubility Index ("NSI") of at least about 75%; and wherein a solution of about 12.0 wt. % of the soy protein isolate in water at a temperature of about 22.degree. C. has a viscosity of less than about 500 centipoise (cp). The isolate is high in saponins and has at least 2.0 mg/g soyasapogenols. The process for producing the soy protein isolate involves removing fiber from a defatted soybean material and obtaining liquor that is subsequently pasteurized. Next, sugars and other small molecular weight components are removed from the liquor using membrane separation with diafiltration while retaining isoflavones and saponins and the resulting retentate is subjected to pasteurization, and optionally spray dried.