Staphylococcus aureus is a notorious human bacterial pathogen that exhibits considerable capacity to develop resistance to antibiotics. We have observed that human infections caused by highly-drug resistant S. aureus are more prolonged, complicated and difficult to eradicate. Here, we describe a novel metabolic adaptation strategy used by clinical S. aureus strains that not only leads to resistance to the last-line antibiotic, daptomycin, but simultaneously impacts host innate immunity. This response was characterized by a change in anionic membrane phospholipid composition induced by point mutations in the phospholipid biosynthesis gene, cls2, encoding cardiolipin synthase. Single cls2 point mutations were sufficient for daptomycin resistance, antibiotic treatment failure and persistent infection. These clinically derived cls2 mutations caused a ‘gain-in-function’ in Cls2, leading to increased bacterial membrane cardiolipin and reduced phosphatidylglycerol, which was linked to changes in membrane structure. The cls2 point mutations also allowed S. aureus to escape from neutrophil chemotaxis, which was secondary to the reduction in bacterial membrane phosphatidylglycerol, a previously undescribed bacterial-driven chemoattractant. Together, these data illustrate a novel metabolic strategy used by S. aureus to promote persistent infection in the face of antibiotic and immune attack, and provide crucial insights into membrane-based therapeutic targeting of this troublesome pathogen.