Bacterial biofilms pose significant challenges in treating infectious diseases due to antibiotic resistance. Finding alternative natural antimicrobial agents is crucial. Bee products, long valued for their nutritional and therapeutic benefits, exhibit potent antibacterial properties. This study investigates bee venom's antibacterial activity against biofilms formed by isolated microorganisms. Biofilm formation of pathogenic bacteria and yeast isolated from cannula was studied using two models: 96-well plates and alginate beads. We showed that low doses of bee venom effectively combat biofilms of bacterial and yeast strains. Antibiofilm assays employed in this study revealed the efficacy of bee venom against biofilms formed by multi-drug resistant Staphylococcus aureus, Pseudomonas aeruginosa and Canndida species isolates. We investigated the potential of bee venom to specifically target pathogenic bacteria while sparing commensal bacteria, showing minimal effects on the commensal bacteria tested in this study. The cytotoxicity of bee venom was evaluated on normal human fibroblast cells (HFB4), revealing a half maximal inhibitory concentration (IC50) of 7 mg/mL, which is substantially higher than the effective antibiofilm dose (0.5 mu g/mL) used against pathogenic bacteria and yeast strains tested in this study. Gene expression analysis further indicated that bee venom treatment influences genes associated with biofilm formation, specifically icaA and icaD in Staphylococcus aureus, as well as genes related to efflux pump activity, including nfxB, which contribute to biofilm persistence in Pseudomonas aeruginosa. Additionally, we employed electron microscopy imaging of single cells and biofilms treated with bee venom to visualize the effects of bee venom. Furthermore, Molecular docking studies employed in this study demonstrate exclusively that bee venom components bind efficiently to antibiotic-resistant determinants, virulence factors, and quorum sensing regulators in the isolated pathogenic bacteria and yeasts, highlighting the need of further explorations into in vivo effects and underlying mechanisms.