This study describes the use of regenerated cellulose (RCA) membranes with molecular weight cut-off (MWCO) values of 10, 30, and 100 kDa, respectively, to separate phytosterols from orange juice for possible nutraceutical production. A desirable membrane separation rejects protein whilst transmitting phytosterols and other low molecular mass compounds such as sugars. The ultrafiltration was performed in a cross-flow membrane system with a total filtration area of 336 cm2. Total phytosterol analysis was carried out by using a Liebermann-Buchard-based method. Protein concentration was quantified by the Bradford method. The effects of three different membranes upon the rejection of total phytosterol content, proteins, sugar, and antioxidant activity were studied. Of the membranes tested, the 10-kDa membrane displayed the highest concentration of phytosterols in the permeate. The 30-kDa and 100-kDa membranes gave comparatively higher phytosterol rejection. The membrane surface roughness and corresponding pure water flux values varied as a function of MWCO such that RCA30 > RCA100 > RCA10. Membranes with rougher surfaces displayed higher fouling than those with smoother surfaces. Hydrophobicity and surface roughness both influenced filtration performance, by controlling the development of the protein-based foulant which modified membrane selectivity.