A simple size-controlled synthesis of cadmium sulfide (CdS) nanoparticle (NP) cores in the cavity of apoferritin from horse spleen (HsAFr) was performed by a slow chemical reaction synthesis and a two-step synthesis protocol. We found that the CdS NP core synthesis was slow and that premature CdS NP cores were formed in the apoferritin cavity when the concentration of ammonia water was low. It was proven that the control of the ammonia water concentration can govern the CdS NP core synthesis and successfully produce size-controlled CdS NP cores with diameters from 4.7 to 7.1 nm with narrow size dispersion. X-ray powder diffraction (XRD), energy dispersive spectroscopy (EDS) analysis and high-resolution transmission electron microscopy (HR-TEM) observation characterized the CdS NP cores obtained as cubic polycrystalline NPs, which showed photoluminescence with red shifts depending on their diameters. From the research of CdS NP core synthesis in the recombinant apoferritins, the zeta potential of apoferritin is important for the biomineralization of CdS NP cores in the apoferritin cavity. These synthesized CdS NPs with different photoluminescence properties will be applicable in a wide variety of nano-applications.