Fructo‐oligosaccharides (FOS) are often produced via enzymatic conversion in industry. Enzyme membrane bioreactor (EMBR) can enhance the catalytic efficiency by in‐situ product removal. Its major bottleneck is the fouling caused by the deposition of enzyme on membrane surface. An EMBR system with a compact rotating disc device was established for continuous FOS production. This study further investigated the influences of the membrane rotation on the flux control and enzyme activity. The speed of 600 rpm was a good compromise between flux and fouling control, which stabilized the flux at ∼80 L m−2h−1 during the process. Moreover, the rotation led to an increase in the rejection of enzymes by 20 %, compensating the loss of enzyme due to the inhomogeneous distribution of membrane pore size.