The Extracellular Vesicle (EV) proteomes of five Staphylococcus aureus (S. aureus) strains originating from human, bovine, and ovine hosts were characterised thanks to proteomics. EVs were purified from supernatants of early stationary S. aureus cultures by a sucrose density gradient. Protein trypsin digestion were performed in solution. The data set contains 15 files of NanoLC-MS/MS analysis, acquired on a Qexactive mass spectrometer. Design: 5 classes (S.aureus human strain: "MW2", S. aureus bovine strains: "NB305" and "RF122", S.aureus ovine strains: "O11" and "O46"). 3 biological replicates.