We have synthesized calcium carbonate nanoparticles (Ca-NPs) in the cavity of a cage-shaped protein, apoferritin, by regulating the electrostatic potential of the molecule. The electrostatic potential in the cavity was controlled by pH changes resulting from changes in the dissolved carbon dioxide (CO2) concentration in the reaction solution. Recombinant L-apoferritin was mixed with a suspension of calcium carbonate (CaCO3), and the mixture was pressurized with gaseous CO2 at 2 MPa. The pH of the solution decreased from 9.3 to 4.4; the CaCO3 dissolved during pressurization, and then precipitated after the pressure was reduced to ambient After repeating the pressurization/depressurization process three times, about 70% of the apoferritin molecules were found to contain nanoparticles with an average diameter of 5.8 +/- 1.2 nm in their cavity. Energy dispersive X-ray spectroscopy and electron diffraction analysis showed that the nanoparticles were calcite, one of the most stable crystal forms of CaCO3. Electrostatic potential calculations revealed a transition in the potential in the apoferritin cavity, from negative to positive, below pH 4.4. The electrostatic potential change because of the change in pH was crucial for ion accumulation. Since the Ca-NPs synthesized by this method were coated with a protein shell, the particles were stably dispersed in solution and did not form aggregates. These Ca-NPs may be useful for medical applications such as synthetic bone scaffolds.