The misuse of antibiotics has led to antibiotic-resistant bacterial strains, making it even harder to combat and eliminate their infections. Staphylococcus aureus causes various adverse infections and diseases, including skin abscesses, bloodstream infections, pneumonia, and joint infections. In this study, we aimed to test the cytotoxic and antibacterial effects of bee venom-loaded chitosan nanoparticles (BV-loaded CS-NPs) in comparison to gamma-irradiated BV and native BV from Apis mellifera. The physiochemical characterizations of our treatments were determined by Fourier Transform Infrared Spectroscopy (FTIR), Transmission Electron Microscope (TEM), zeta-potential, release rate, and Encapsulation Efficiency (EE). Our study was conducted on both levels, in-vitro and in-vivo. For the in-vitro study, a bacterial model of Staphylococcus aureus with an ATCC number of 6538 was grown in tryptic soy agar (TSA) medium, and the inhibition zones of our drug candidates were measured with the appropriate statistical analysis performed. For the in-vivo study, levels of aspartate aminotransferase (AST), alanine aminotransferase (ALT), Creatinine, Urea, and interleukin 6 (IL-6) were analyzed. BV-loaded CS-NPs showed relatively better results than the other alternatives, which are native BV and gamma-irradiated BV. The results showed that the antibacterial effect of BV-loaded CS-NPs was greater than the alternatives. Furthermore, its cytotoxic effect was far less than the native and irradiated bee venom. These outcomes ensure that loading BV on CS-NPs makes it a promising drug candidate for an antibiotic alternative with minimal cytotoxicity and enhanced antibacterial activity.