Organic–inorganic hybrid microcapsules (AP-capsules) were fabricated by sequential preparation of calcium alginate microcapsules (Alg-capsules), followed by the addition of the Alg-capsules to an aqueous solution of 3-aminopropyltriethoxysilane (APTES) in mild conditions without the use of any catalyst. Results showed that the shell thickness of AP-capsules was found to vary with time during the APTES incorporation onto the Alg-capsules, suggesting that the shell thickness was dependent on the amount of CaCl2 contained initially in the core solution as well as on the reaction time. A model enzyme, formate dehydrogenase (FDH), was successfully encapsulated in AP-capsules, and maximum efficiency of encapsulation was found with the capsule size of 1 mm diameter. The AP-capsules were reused efficiently for 10 cycles without loss of FDH activity. The approach developed in this study could evolve as a generic platform of enzyme immobilization for biotechnology applications using core–shell microcapsule technology.