The central composite design with a quadratic model was used to investigate the effect of temperature (20–40 °C) and transmembrane pressure (TMP) (100–300 kPa) as well as pretreatment with gelatin and bentonite (0:0–300:1500 mg L−1) on permeate flux and fouling resistance during ultrafiltration of apple juice. The changes in some physicochemical properties were also investigated. Pretreatment of apple juice with gelatin and bentonite and an increase in the temperature and TMP significantly improved the permeate flux. In general, physicochemical properties of apple juice other than polyphenolics were not affected by the applied parameters. Using 150 mg L−1 of gelatin and 750 mg L−1 of bentonite for fining significantly reduced the total phenolic content and so did the fouling resistance. Fouling resistance also decreased with increasing temperature, and increasing pressure increased the fouling resistance.