Biofilm formation in the resin-composite interface is a major challenge for resin-based dental composites. Using doped z nanoparticles (NPs) to enhance the antibacterial properties of resin composites can be an effective approach to prevent this. The present study focused on the effectiveness of Selenium-doped ZnO (Se/ZnO) NPs as an antibacterial nanofiller in resin composites and their impact on their mechanical properties. Pristine and Se/ZnO NPs were synthesized by the mechanochemical method and confirmed through UV-Vis Spectroscopy, FTIR (Fourier Transform Infrared) analysis, X-ray Diffraction (XRD) crystallography, Scanning Electron Microscopy (SEM), Energy Dispersive Spectroscopy (EDS), and Zeta analysis. The resin composites were then modified by varying concentrations of pristine and Se/ZnO NPs. A single species (S. mutans and E. faecalis) and a saliva microcosm model were utilized for antibacterial analysis. Hemolytic assay and compressive strength tests were also performed to test the modified composite resin’s cytotoxicity and mechanical strength. When incorporated into composite resin, 1% Se/ZnO NPs showed higher antibacterial activity, biocompatibility, and higher mechanical strength when compared to composites with 1% ZnO NPs. The Se/ZnO NPs has been explored for the first time as an efficient antibacterial nanofiller for resin composites and showed effectiveness at lower concentrations, and hence can be an effective candidate in preventing secondary caries by limiting biofilm formation.