A novel method was developed for papain immobilization through a biomimetic silicification process induced by papain. By incubating papain in a silica precursor solution, the papain-silica composite formed rapidly and papain was encapsulated. The encapsulation efficiency and the recovery activity were 82.60% and 83.09%, respectively. Compared with enzymes and biomolecules immobilized in biosilica matrix in the presence of additional silica-precipitating species, this papain encapsulation process, a biomimetic approach, realized high encapsulation efficiency by its autosilification activity under mild conditions (near-neutral pH and ambient temperature). Furthermore, the encapsulated papain exhibits enhanced thermal, pH, recycling and storage stabilities. Kinetic analysis showed that the biomimetic silica matrix did not significantly hinder the mass transport of substrate or the release of product.