Intact skin is the first physical barrier against all microbial infections. Thus, in the cases of wounds, burns, and skin damage, bacteria can infect and invade the deeper layers of skin to the bloodstream and other organs leading to severe illnesses. Thus, our study aims to investigate the potential activity of natural products, propolis and honeybee venom, to control wound infections with multi-drug resistant Staphylococcus aureus (MDRSA) and safely accelerate the wound healing. First, this study characterized the clinically isolated S. aureus using biochemical, molecular, and antibiotic sensitivity tests. Then, the hydrogel was prepared via mixing chitosan with honey, propolis, and venom at different ratios, followed by physicochemical characterization and biological examination. The in vivo experiment results after topical application of optimum concentrations revealed that both venom and propolis have significant antibacterial activity at different temperatures. The IC50 of both propolis antioxidant and cytotoxicity assays was found to be 40.07 ± 2.18 μg/mL and 18.3 μg/mL, respectively. The cocktail bacteria showed both minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) of 10 µg/mL and of 300 µg/mL with venom respectively & MIC and MBC of 100 µg/mL, 300 µg/mL with propolis respectively. The use of hydrogel was effective against wound infection and enhanced wound healing during 14 days. Before starting clinical trials, further studies can be done on large animal models.