Staphylococcus aureus colonizes 30% of the human population, but only a few clones cause severe infections. S. aureus’ virulence varies and partly depends on the presence of prophages, viral DNA embedded in the S. aureus core genome, such as hlb-converting prophage (ϕSa3int). Human-adapted S. aureus often harbours a ϕSa3int prophages preferentially integrated into their b-hemolysin (hlb) gene that encodes human immune evasion cluster (IEC) genes. To study the effects of ϕSa3int prophages, we induced the ϕSa3int prophage from one of the clinical isolates, transduced it into the Sa3int-prophage-free strain and studied their behaviour using sequencing as well as mass spectrophotometry. Integration of ϕSa3int prophage down-regulated the beta-hemolysin expression of the lysogen. In silico analysis of the S. aureus genome confirmed the insertion of a ~43.8 kb ϕSa3int prophage into hlb gene. However, acquiring ϕSa3int prophage significantly changed the expression of various secreted proteins, both bacterial and prophage-encoded. Altogether, thirty-eight exoproteins were significantly differentially regulated in the laboratory-created lysogen, compared to its recipient strain. Among these proteins, there was significant upregulation of 21 exoproteins (55.3 %) including staphylokinase (sak), SCIN (scn), and intercellular adhesion protein B (icaB) and downregulation of 17 exoproteins (44.7 %), including b-hemolysin (hlb/sph) and outer membrane porin (phoE). Most of the upregulated proteins were involved in immunomodulation that help S. aureus escape human innate immunity and help cause chronic infection. These findings may contribute to developing novel approaches to render S. aureus susceptible to the immune response by blocking prophage-associated defence mechanisms.