A high quality soy protein isolate with a significant reduction in phytate and aluminum is prepared via ultrafiltration. Defatted soy flour slurry is prepared and adjusted to a pH such that the protein becomes solubilized. The solubilized protein can pass through the ultrafiltration membrane. The ultrafiltration system rejects phytate and aluminum. Once the soluble protein passes through the ultrafiltration system the soy protein isolate is then precipitated from the clear permeate stream by adjusting the pH within the isoelectric range of soy proteins.