Mechanisms for cellular detoxification of drug compounds are of significant interest in human health. Cyclosporine A (CsA) and tacrolimus (FK506) are widely known antifungal and immunosuppressive microbial natural products. However, both compounds can result in significant side effects when used as immunosuppressants. The insect pathogenic fungusBeauveria bassianashows resistance to CsA and FK506. However, the mechanisms underlying the resistance have remained unknown. Here, we identify a P4-ATPase gene,BbCRPA, from the fungus, which confers resistanceviaa unique vesicle mediated transport pathway that targets the compounds into detoxifying vacuoles. Interestingly, the expression ofBbCRPAin plants promotes resistance to the phytopathogenic fungusVerticillium dahliaevia detoxification of the mycotoxin cinnamyl acetate using a similar pathway. Our data reveal a new function for a subclass of P4-ATPases in cell detoxification. The P4-ATPases conferred cross-species resistance can be exploited for plant disease control and human health protection.