The purpose of this study was to concentrate the polyphenolic compounds in pistachio hull extract as a rich source of natural antioxidants using the membrane process and the reduction of membrane fouling during the process. After the optimization of the membrane performance includes chamber pressure and stirring rate by monitoring flux and membrane fouling, pectinase and tannase enzymes were compared in order to reduce fouling. Pectinase showed a better potential in decreasing membranous fouling. Enzyme concentration was optimized, and treatment with 17.4 (U) was selected. The permeate obtained from optimized membrane condition and enzyme level treatment was enriched in total phenol (120.31 ± 0.35 mgGAE/g) and flavonoid (34.54 ± 0.09 mgCE/g), while the amount of anthocyanin was not remarkable.