Enzymatic conversion processes face challenges in controlling oligosaccharide molecular weight (Mw). Enzymatic membrane reactors (EMRs) with immobilized enzymes address this, but direct enzyme immobilization on the membrane surface can lead to deactivation and reduced hydrolysis efficiency. This study proposes a novel EMR configuration: a three-layer structure. An electrospun porous fibrous layer, modified with PDA, TA, and APTES, serves as a mechanical support layer. A commercial separation membrane is positioned below. This configuration enhances enzyme activity and selectivity. Using a “fouling-induced” technique, immobilized activity of the enzyme (i.e. dextranase) significantly increased to 11.5 µmol-isomaltose/min, surpassing incubation-immobilized dextranase (0.075 µmol-isomaltose/min). The additional layer preserves catalytic patterns, reducing fouling and ensuring high selectivity. The EMR configuration excels in producing low Mw oligosaccharides. The catalytic layer achieves 11.3 µmol-isomaltose/min, while the membrane exhibits exceptional selectivity and stability. The hydrophilic RC10 membrane with small pores performs best. This study highlights the potential of the EMR system for efficient production of stable low Mw oligosaccharides. Insights into optimizing enzyme immobilization strategies and membrane selection benefit enzymatic conversion processes.