Biocatalytic membranes (BMs) have promising applications in a diversity of fields including food, pharmaceutical and water treatment industries. Of particular relevance, Alcalase is a commercially important protease that has been applied for the production of peptides from the hydrolysis of proteins. In this study, two different approaches were applied for the modification of electrospun polyacrylonitrile nanofibrous membranes (EPNMs) for Alcalase immobilization. The first approach is alkali modification of EPNMs followed by EDC/NHS coupling for covalent bonding with Alcalase, whereas the other is based on polydopamine coating with or without glutaraldehyde grafting as a covalent linker. Immobilized Alcalase on these prepared BMs were studied and compared with free enzymes. It was found that the stabilities of Alcalase on BMs created using both approaches were improved, which enabled their reuse of 10 cycles with significant retention of enzymatic activity. A continuous reactor housing BMs were tested for hydrolysis of both model substrate, azo-casein and soybean meal protein (SMP). It was found that decreasing flux could improve the extent of hydrolysis and that a single-layer reactor can hydrolyze about 50% of the substrate to peptides with the molecular weight of 10 kDa or less. Hydrolysis of SMPs was demonstrated in a continuous five-layer BM reactor and both BMs showed excellent hydrolysis capacity. This study provides the groundwork for the development of high-efficiency BM for continuous and cost-effective protein hydrolysis for the production of value-added peptides.