The overuse of antibiotics has accelerated the emergence of resistant bacteria, posing critical threats to food safety and public health. This challenge underscores the urgent need for alternative strategies, such as antivirulence therapy, which disarms pathogens by targeting virulence factors rather than inhibiting bacterial growth. In this study, we identified farrerol, a flavonoid, as a potent inhibitor of the caseinolytic peptidase P (ClpP) protease, a key virulence regulator in Staphylococcus aureus, with an IC₅₀ of 19.33 μg/mL. Farrerol significantly disrupts virulence factor secretion and reduces pathogenicity, demonstrating its potential to control S. aureus-induced foodborne illnesses. Mechanistic studies using fluorescence resonance energy transfer (FRET), thermal shift assay (TSA), cellular thermal shift assay (CETSA), fluorescence quenching, and molecular docking revealed that farrerol interacts with ClpP via key residues (GLY-127, GLN-132, and ASP-170). In vivo, farrerol reduced the bacterial load and improved survival in a Galleria mellonella infection model. Our findings demonstrated that farrerol is an effective antivirulence agent, offering an innovative approach for the food industry to control S. aureus-induced foodborne infections. This approach holds great potential for enhancing food safety and mitigating antibiotic resistance.