Abstract Immunoglobulin G (IgG) was immobilized on a stack of microporous cation‐exchange membranes and pulsed with pepsin solution. Fc fragment and its sub‐fragments thus produced were removed along with the reaction flow‐through, whereas F(ab′) 2 which remained membrane bound could subsequently be eluted in a pure form using salt. The extent of IgG fragmentation and the apparent reaction rate constant were both significantly higher than in equivalent liquid phase reaction, presumably due to a combination of mass transport, steric, and substrate concentration effects. This approach of using a membrane surface as molecule cutting board could be attractive in niche applications such as integrated enzymatic reaction and purification processes involving macromolecular substrates. © 2010 American Institute of Chemical Engineers Biotechnol. Prog., 2011