The optimal conditions for the recovery of an enzyme were determined using gas/liquid two-phase flows. When filtering the enzyme-only solution under single-phase flow conditions, a severe fouling occurred. This fouling was manifested as a decline in enzyme mass flux due to a decrease in both flux and transmission. When yeast cells were added under the same experimental conditions, the enzyme mass flux was nearly twofold higher. During gas-sparged microfiltration of the enzyme/yeast mixture in a permeate-recycling mode at the same liquid flow rate, gas/liquid slug flow strongly decreased the mass flux of the enzyme due to the drastic reduction in transmission (70% decrease) even though the permeate flux was improved (140% improvement). However, with a bubble flow pattern, the enzyme mass flux was 25% higher (flux slightly enhanced and high transmission), and during the diafiltration experiment a 13% higher enzyme recovery was achieved.