Mesenchymal stromal cells (MSCs) from various species, such as humans, mice, and horses, were recently found to effectively inhibit the growth of various bacteria associated with chronic infections, such as nonhealing cutaneous wounds, via secretion of antimicrobial peptides. These MSC antimicrobial properties have primarily been studied in the context of the planktonic phenotype, and thus, information on the effects on bacteria in biofilms is largely lacking. The objectives of this study were to evaluate the in vitro efficacy of the MSC secretome against various biofilm-forming wound pathogens, including the methicillin-resistant Staphylococcus aureus (MRSA), and to explore the mechanisms that affect bacterial biofilms. To this end, we used equine MSCs, because the horse represents a physiologically relevant model for human wound healing and offers a readily translatable model for MSC therapies in humans. Our salient findings were that the equine MSC secretome inhibits biofilm formation and mature biofilms of various bacteria, such as Pseudomonas aeruginosa, S. aureus, and Staphylococcus epidermidis. Furthermore, we demonstrated that equine MSC secrete cysteine proteases that destabilize MRSA biofilms, thereby increasing the efficacy of antibiotics that were previously tolerated by the biofilms. In light of the rise of antibiotic-resistant bacterial strains as an increasing global health threat, our results provide the rationale for using the MSC secretome as a complementary treatment for bacterial skin infections in both humans and horses.