In this work, the use of a pH-responsive isoporous membrane allowed the compartmentalization of two different enzymes, one on the surface and the other in the pores of the membrane. This intensified and compartmentalized enzyme-loaded membrane system allowed the two enzymatic reactions to be modulated based on a pH shift. The chosen enzymes are pectinase and β-glucosidase, enzymes commonly used in biorefinery, whose optimum pH (3 and 6.5, respectively) is in the range where membrane pore closing (pH < 4) and opening is observed. Pectinase is covalently bound to the membrane surface at pH 3 while the pores are closed and is used to control the membrane fouling due to pectin accumulation during plant material processing. β-glucosidase is immobilized in the membrane pores at pH 6.5 (open pores) and is used to catalyze the reaction of oleuropein into the phytotherapeutic oleuropein aglycone. The different localization of the two enzymes was demonstrated by AFM, immunolocalization and SEM, confocal microscopy and XPS. In the open pore configuration, a very high conversion of pectin and oleuropein is simultaneously obtained (93% and 95%, in 165 h, respectively); whereas, in the closed pore configuration, an increased and exclusive conversion (95% in 24 h) of pectin was obtained. This innovative strategy of artificial ordered compartmentalization allows tuning the enzymatic reactions based on pH, preserving labile biomolecules (e.g.β-glucosidase) from deactivation at acidic pH and cleaning the membrane avoiding aggressive solvents. This makes it possible to increase the stability of enzymes, which is an obstacle to the development of biocatalytic membrane reactors, and proposes an unconventional and efficient way to synchronize the action of complementary enzymes in a case, or to selectively enhance the action of one of them by simply shifting the pH.