A biocompatible interface was constructed on a microchip by using the layer‐by‐layer (LBL) assembly of charged polysaccharides incorporating proteases for highly efficient proteolysis. The controlled assembly of natural polyelectrolytes and the enzyme‐adsorption step were monitored by using a quartz‐crystal microbalance and atomic force microscopy (AFM). Such a multilayer‐assembled membrane provides a biocompatible interconnected network with high enzyme‐loading capacity. The maximum digestion rate of the adsorbed trypsin in a microchannel was significantly accelerated to 1600 mM min−1 μg−1, compared with the tryptic digestion in solution. Based on the Langmuir isotherm model, the thermodynamic constant of adsorption K was calculated to be 1.6×105 M−1 and the maximum adsorption loading Γmax was 3.6×10−6 mol m−2, 30 times more than a monolayer of trypsin on the native surface. The tunable interface containing trypsin was employed to construct a microchip reactor for digestion of femtomoles of proteins and the produced peptides were analyzed by MALDI‐TOF mass spectroscopy. The efficient on‐chip proteolysis was obtained within a few seconds, and the identification of biological samples was feasible.