This paper introduces a practically useful approach for fabrication of hydrogel microcapsules layered with a mechanically robust polyelectrolyte/silica thin shell. For this, monodisperse negatively charged hydrogel microparticles were fabricated combining the microfluidic technique and subsequent photopolymerization. Then, alternate polyelectrolyte layers were generated onto the microparticles by using the layer-by-layer deposition. In the final stage, reduction of silicate on the polyelectrolyte layer was conducted to form a silica layer on the outermost layer of the shell. Uniform covering of the periphery of the hydrogel microparticles with the hybrid shell layer was confirmed by SEM and EDX analyses as well as by improved structural shell resistance to osmolality. The thickness of the shell layer was detected by approximately one micrometer. Finally, we demonstrated that the polyelectrolyte/silica hybrid shell showed remarkably low permeability against smallmolecules, which allows us to explore microcapsule applications toward complete segregation and stabilization of water-soluble active molecules.