Glycinin-rich and â-conglycinin-rich products are prepared by soy protein fractionation. Physicochemical characteristics of these proteins affect their unique, important functionality in food systems and industrial applications. Soybean isoflavones and saponins are phytochemicals with potential health benefits. Objectives of this protein fractionation research were to (1) improve protein and phytochemical extraction from defatted soy flakes and recovery in product fractions and (2) evaluate phytochemical partitioning and profile changes during fractionation. Extraction environments (pH, ethanol concentration, temperature, and water-to-flake ratio) were each varied during bench-scale optimization. Optimized conditions of 45 °C and 10:1 water-to-flake ratio were compared with previous conditions of 20 °C and 15:1 water-to-flake ratio and a soy protein isolate process at pilot scale. Optimized conditions yielded more â-conglycinin with higher isoflavone and saponin concentrations, but fraction purity was diminished by glycinin contamination. Bench-scale data demonstrated that increased phytochemical extraction did not translate into increased concentrations in product fractions.