Appropriately designed and operated enzyme membrane bioreactors (EMBRs) can fully utilize the activity of free, soluble enzymes while maximizing enzyme reusability and simultaneously removing the enzyme-free product in situ. A filtration model system was applied to determine critical EMBR design factors suitable for continuous enzymatic production of prebiotic fructo-oligosaccharides. The filtration flux and separation efficiency were investigated in terms of the membrane cutoff rating. In addition, the influence of operational conditions on enzyme activity was also determined.