In the present study, we report on the carbonic anhydrase (CA)-assisted formation of biomineralized calcium carbonate crystalline composites (CCCCs). Ellipsoidal CCCCs, such as calcite polymorphism, in a micro-size range catalyzed by CA were successfully synthesized with polyethylene glycol and magnetic nanoparticles in the constant CO2 pressure controlled chamber, for the first time. CA-assisted CCCCs characterized by X-ray diffraction, transmission electron microscopy, scanning electron microscopy, and dynamic light scattering, showed their crystalline phase with mesoporous property according to Fourier transform infrared and Brunauer–Emmett–Teller area. These CCCCs retained about 43% of free CA esterase activity. Furthermore, the magnet-based separation was also successful for the reuse of the CCCCs. As a result, the CCCCs produced preserved their catalytic activity even after its ten repeated usages, and were stable for more than 50 days under room temperature. The reported method paves the way for novel biomineralization via CA for the formation of functional CA containing nanocomposites and biocatalyst technology applications.