Diverse organisms secrete amphipathic biomolecules for competitive gains. However, how cells cope with producing these membrane-permeabilizing molecules is unclear. We focused on the PSM family of secreted amphipathic peptides in the pathogen Staphylococcus aureus that uses two ABC transporters, PmtCD and AbcA, to export peptides across the bacterial cell membrane. We found that increased peptide hydrophobicity favors PSM secretion through PmtCD over AbcA and that only PmtCD protected cells against amphipathic peptides. We propose a two-system model in which PmtCD and AbcA independently export PSMs from either membrane or cytosolic environments, respectively. Our model provides a rationale for the encoding of multiple transport systems on diverse biosynthetic gene clusters used to produce distinct amphipathic molecules. In addition, our data serve as a guide for selectively blocking PSM secretion to achieve antimicrobial or antivirulence approaches and to disrupt established roles of PSM-mediated virulence.