Ensuring the effective antibacterial with enhanced cytocompatibility of zinc oxide (ZnO) nanomaterials is still a challenging task. Here, we initially coated ZnO NPs with polydopamine (PDA), then integrated hydroxyapatite (HAp), and eventually obtained HAp@ZnO/PDA composite NPs to investigate the cytocompatible and antibacterial properties of the NPs in terms of different concentrations (200 to 6.25 µg/mL). The morphological analysis confirmed that the PDA-coating assisted the facile integration of HAp on the surface of ZnO/PDA NPs, and successfully synthesized the HAp@ZnO/PDA-06, HAp@ZnO/PDA-12, and HAp@ZnO/PDA-24 NPs by varying the modified-simulated body fluid (m-SBF) incubation time. Moreover, the morphological analysis also acknowledged that the prolonged incubation period (i.e., more than 6 h) is not recommendable for better HAp integration. Similarly, the antibacterial test confirmed that all three types of HAp@ZnO/PDA composite NPs including pure ZnO and ZnO/PDA NPs exhibited dose-dependent bactericidal action, and they were more efficient against Gram-positive Staphylococcus aureus compared to Gram-negative Escherichia coli. According to the results, the average E. coli survival percentage on pure ZnO, ZnO/PDA, HAp@ZnO/PDA-06, HAp@ZnO/PDA-12, and HAp@ZnO/PDA-24 NPs at the concentration range from 200 to 6.25 µg/mL was around 52%, 59%, 59%, 57%, and 55% respectively while the average S. aureus survival percentage on those NPs at the concentration range from 200 µ to 6.25 µg/mL was around 37%, 45%, 47%, 45%, and 41% respectively. In terms of cytocompatibility, the HAp@ZnO/PDA NPs treated samples showed enhanced MC3T3-E1 cell adhesion and proliferation when compared to pure ZnO NPs. The result explained that in all the tested NPs above 50 µg/mL, the cell viability is less than 50% while the concentration of NPs below 50 µg/mL showed more than 100% of cell viability, and at 50 µg/mL, the cell viability exhibited by pure ZnO, ZnO/PDA, HAp@ZnO/PDA-06, HAp@ZnO/PDA-12, and HAp@ZnO/PDA-24 composite NPs was 42%, 75%, 83%, 78%, and 70% respectively in average. Moreover, the cell viability reached above 350% in the 6.25 µg/mL of NPs treated samples. Hence, the study concluded that preparing HAp@ZnO/PDA composite NPs following mussel-inspired PDA coating and simulated body fluid (SBF) incubation techniques provided a facile way for the enhancement of the cytocompatibility of ZnO NPs without losing its potential antibacterial properties.