Infections during or after the denture filling pose a serious threat to recovery later, and antibiotics are scanty for quick healing. The antibacterial potential of Zn has convinced us to fabricate its composites with hydroxyapatite (HA), which has distinct biological properties. The main aim of the study is to evaluate the antibacterial potential of Zn-doped HA and investigate its molecular interaction with bacterial strains to enhance its defensive ability against bacterial attack. This study investigates the synthesis of zinc-doped hydroxyapatite nano-powder (Zn-HA) as coating and filling materials for dental applications. The co-precipitation technique was used in this regard to obtain the purest form of nanoparticles. The as-prepared Zn-HA samples were characterized by FTIR spectroscopy to assess the interaction of functional groups between components, x-ray diffraction (XRD) to determine percentage crystallinity, SEM to explore the surface morphology of composites, and EDX to confirm the incorporation of Zn in the apatite structure. The crystalline size of Zn-HA decreases from 99 nm to 40 nm with an increase in the doping of Zncl2 from 0 to 2.5 g. With increasing the concentration of Zn doping, the effectiveness of antibacterial potential was increased. Due to an increased in the concentration of doped Zn, the Zn ions effectively rupture the bacterial membrane and destroy its DNA. Meanwhile, it shows the highest antibacterial activity against Pseudomonas (20.2 ± 0.02), Klebsiella (25.8 ± 0.05), Bacillus (18.3 ± 0.09), S. aureus (24 ± 0.03), and E. coli (19.3 ± 0.09) with Zn/HA5. It showed that by increasing the concentration of Zinc ions in hydroxyapatite, the antibacterial potential increased. This increased concentration of zinc ions in HA enhances its-defensive ability against the attack of various bacterial strains, this makes it a potential material and enhances its efficacy in dental applications like coating, filling material, or dental restoratives, in inhibiting the growth of bacterial colonies and biofilm formation in the oral cavity. In this way, Zn/HA as an efficient dental composite as a restorative material with enhanced antibacterial potential may help to mitigate the risk of dental infections, promote dental as well as oral health, and overall improve the life of dentine.