A novel approach to the synthesis of protein microcapsules is developed through template-mediated interfacial reaction. Protein-doped CaCO3 templates are first synthetized via coprecipitation and then coated with a catechol-containing alginate (AlgDA) layer. Afterward, the templates are exposed to ethylenediamine tetraacetic acid disodium (EDTA) solution to dissolve CaCO3. During CaCO3 dissolution, the generated CO2 gas pushes protein molecules moving to the AlgDA layer, and thereby Michael addition and Schiff base reactions proceed, forming the shell of protein microcapsules. Three kinds of proteins, namely, bovine serum albumin, catalase, and protamine sulfate, are utilized. The shell thickness of microcapsule varies from 25 to 82 nm as the doping amount of protein increased from 2 to 6 mg per 66 mg CaCO3. The protein microcapsules have a robust but flexible shell and can be reversibly deformed upon exposure to osmotic pressure. The bioactivity of protein microcapsules is demonstrated through enzymatic catalysis experiments. The protein microcapsules remain about 80% enzymatic activity of the equivalent free protein. Hopefully, our approach could be extended to many other applications such as drug/gene delivery, tissue scaffolds, and catalysis due to the universality of Michael reaction and Schiff base reactions.