Recently, zinc-based materials have gained immense attention as antimicrobial agents. In this study, zinc-doped mesoporous hydroxyapatites (HAps) with various Zn contents were prepared by co-precipitation using a phosphoprotein as the porous template. The use of the phosphoprotein as the porous template resulted in the formation of zinc-doped mesoporous HAps (mHAps) with large pores and specific surface area (182 m2 g−1), as indicated by the nitrogen adsorption/desorption measurements. The formation of the zinc-doped HAps was confirmed by various analytical techniques such as X-ray diffraction, Fourier transform infrared spectroscopy, transmission electron microscopy, and X-ray photoelectron spectroscopy. The biomaterials prepared in this study were used as antimicrobial agents against gram-positive (Staphylococcus aureus) and gram-negative (Escherichia coli) bacteria. The Zn2%–mHAp sample showed the maximum bacterial inhibitory concentrations of 50 ± 5% and 77 ± 5% for the Gram-positive and Gram-negative bacteria, respectively. The antibacterial activity of the mHAp samples depended strongly on their Zn2+ content. Thus, the use of a biotemplate and Zn2+ ions is an efficient approach for the formation of novel HAp-based biomaterials with promising antibacterial properties. This synthesis approach will pave a new pathway for the functionalization of other materials for different biomedical applications.