The organic–inorganic hybrid materials have been used in different fields to immobilize biomolecules since they offer many advantages. The aim of this study was to optimize and characterize the alginate‐silica hybrid hydrogel as a stable and injectable form for microfluidic systems using internal gelation method and increase the stability and activity of immobilized enzyme for biocatalytic conversions as well. Characterization was carried out by scanning electron microscopy, energy dispersive spectroscopy/mapping, Brunauer–Emmett–Teller, Barrett–Joyner–Halenda, and Fourier‐transform infrared spectroscopy analyses, and the shrinkages of monoliths were evaluated. Subsequent to optimizing the enzyme concentration (40 μg), hydrolytic conversion of 4‐nitrophenyl β‐d‐glucopyranoside (pNPG) was performed to understand the behavior of the bioconversion in the microfluidic system. The yield was 94% which reached the equilibrium at 24 h indicating that the alginate‐silica gel derived microsystem overcome some drawbacks of monolithic systems. Additionally, bioconversion of Ruscus aculeatus saponins was carried out at the same setup in order to obtain aglycon part, which has pharmaceutical significance. Although pure aglycon could not be achieved, an intermediate compound was obtained based on the HPLC analysis. The developed formulation can be utilized for various life science applications.