Recently, postoperative bone infections have been one of the most crucial challenges for surgeons. This study aims to synergistically promote antibacterial and osteoconductive properties of hydroxyapatite (HAp) nanoparticles through binary doping of Zn2+ and Ga3+ ions (Zn-Ga:HAp). Zn-Ga:HAp nanopowders with spherical morphology and homogeneous size are synthesized using a simple sol-gel method. Substitution of both zinc and gallium in the structure of HAp results in a gradual decrease in the lattice parameters as doping level increases, limits the growth of HAp particles and reduces its crystallinity. Noticeably, the crystallinity of HAp (85%) reduces to less than 73% (for XZn = 0.1), 78% (for XGa = 0.4) and 75% (for XZn = 0.1 and XGa = 0.4). Ion doping also significantly modulate the release of bioactive ions (Ca2+, PO43−, Zn2+, Ga3+) from the Zn-Ga:HAp depended on the overall amount of Ga and Zn in the HAp, which could mediate the biological responses. Incorporating both Zn2+ and Ga3+ ions in HAp structure could significantly improve the antibacterial activity of HAp nanopowders against Staphylococcus aureus (S. aureus) and Escherichia coli (E. coli) with a concentration-dependent effect. Noticeably, Zn-Ga:HAp (XZn = 0.1 and XGa = 0.4) powder shows the antibacterial activity of more than 68% and 84% against E. coli and S. aureus, respectively, at the concentration of 500 μg/ml, thereby showing excellent antibacterial properties. In addition, Zn-Ga:HAp nanopowders not only do not exhibit any cytotoxicity towards hMSCs, but also show significantly superior osteogenic properties. For instance, Zn-Ga:HAp (XZn = 0.1 and XGa = 0.4) nanopowders significantly enhance the alkaline phosphatase activity (approximately 2-fold) and mineralization (approximately 3-fold) of hMSCs after 14 days of culture, compared to pure HAp. Overall, Zn-Ga:HAp (XZn = 0.1 and XGa = 0.4) with desired osteogenesis and antibacterial activity compared to pure HAp, Zn:HAp and Ga:HAp shows promising opportunities for the implant-associated infections and the efficient healing of bone defects.