Inspired by the biological cell structure, a novel and facile method for preparing organic–inorganic composite microcapsules is developed by a synergy of layer-by-layer (LBL) self-assembly and biomimetic mineralization. The LBL microcapsule is fabricated by the alternative assembly of a negatively charged polyelectrolyte, poly(styrene sulfonate) (PSS), and a positively charged biomacromolecule, protamine (Pro), onto calcium carbonate microparticles. An inorganic silica layer is then constructed through a biomimetic mineralization process induced by the outer protamine layer. Catalase is captured in the CaCO₃ templates via co-precipitation and encapsulated in the composite capsules followed by dissolution of the templates. TEM and confocal laser scanning microscopy (CLSM) observations show that the microcapsules possess a hollow structure and the enzyme inside exists in a free state. The morphology and chemical composition of the microcapsules are characterized by SEM, FTIR and NMR. The dual role of protamine as both a positive layer component and an inducer for silicification provides a simple and efficient approach to form a microbioreactor with a complete, uniform and robust outer shell. Compared to the Pro/PSS LBL microcapsule, the encapsulation efficiency, harsh condition tolerance and long-term storage stability of the encapsulated enzyme are all notably improved due to the shielding effect of the inorganic shell. The fabrication method presented here may provide a general strategy for the preparation of composite materials whose structure of organic membrane and inorganic shell could be easily tuned by varying the LBL and mineralization conditions.