Cold atmospheric plasma (CAP) has been demonstrated to be a successful antiseptic for chronic and infected wounds. Although experimental work has focused on elucidation of the curative power of CAP for wound healing, the molecular mechanisms behind this ability are less understood. To date, the direct effect of CAP on the activity of microbial virulence factors has not been investigated. In the present study, we therefore examined whether CAP can modulate the detrimental activity of M1 protein, one of the most studied <i>Streptococcus pyogenes</i> virulence determinant. Our results show that CAP abolishes the ability of M1 protein to trigger inflammatory host responses. Subsequent mass spectrometric analysis revealed that this effect was caused by oxidation of Met81 and Trp128 located at the sub-N-terminal region of M1 protein provoking a conformational change. Notably, our results also show that CAP has an insignificant effect on the host immune system, supporting the benefits of using CAP to combat infections. Considering the growing number of antibiotic-resistant bacteria, novel antimicrobial therapeutic approaches are urgently needed that do not bear the risk of inducing additional resistance. Our study therefore may open new research avenues for the development of novel approaches for the treatment of skin and wound infections caused by <i>S. pyogenes</i>.