Carbonic anhydrase (CA) is a powerful green catalyst for CO2 capture and utilization due to its ultrafast kinetics and biobased nature. For industrial utilization, immobilization of CA is needed to increase enzyme stability and recovery. Diatom-inspired silica nanoparticle provides a green platform for the efficient immobilization of enzymes in a fast and facile manner. Herein, we describe a simple and effective method of salt addition during diatom-inspired silicification for the development of an immobilized and highly stabilized catalyst with bovine CA (bCA). Silica synthesis was facilitated by the silica-forming R5 peptide fused to the bCA; bCA-R5 was immobilized in situ with an excellent immobilization yield. The thermal stability of bCA-R5 was improved via salt supplementation, which was controlled by the cation-assisted increase in silica synthesis with a high packing density. The salt effect was dependent on both the pH and the enzyme’s electrostatic nature, suggesting the interplay among all the reaction components. The thermal stability of immobilized bCA-R5 was improved 11-fold in a biological buffer and 18-fold in 4.2 M MDEA (an organic solvent used as a CO2 absorbent) via the cation-assisted method. The suggested strategy is useful for developing CO2-capturing nanomaterials and can be widely applicable to immobilizing and stabilizing various proteins, maximally exploiting the potential of diatom-inspired silicification.