Earth-abundant mineral limestone obtained from North Sumatera, Indonesia, has been utilized to synthesize nano-hydroxyapatite (HAp). Although HAp is biocompatible to the human bone, its antibacterial activity is still very low. Herein, different metal ions (i.e., Ag, Cu, Zn, and Mg) were doped into HAp to improve the antibacterial activity. The as-synthesized HAp was characterized by X-ray ray diffraction (XRD), field-emission scanning electron microscope (FE-SEM), energy disperse spectroscopy (EDS), Fourier transmission infrared spectroscopy (FTIR), X-ray photoelectron spectroscopy (XPS), and Brunauer–Emmett–Teller (BET). The antibacterial test showed that the performance of HAp to inactivate bacterial growth was significantly improved after incorporating the metal ion dopants into HAp. Ag-HAp exhibited the highest activity toward E. coli and S. aureus with an antibacterial rate of 99.9 ± 0.1%, followed by Zn-HAp, Cu-HAp, and Mg-HAp.