Staphylococcal scalded skin syndrome (SSSS) is a life-threatening skin condition caused by Staphylococcus aureus (SA) strains producing exfoliative toxin. Most SSSS cases are associated with Exfoliative Toxin A, encoded by the eta gene and carried by a temperate bacteriophage phiETA (ΦETA). An estimated ~10% of strains containing ΦETA are methicillin-resistant SA (MRSA), raising questions about the factors associated with ΦETA susceptibility. Our study investigates the lysogenization susceptibility of ΦETA in a set of SA strains through lysogenic challenges. To this end, we first isolate phage lysates from a known epidemic strain containing eta. In lysogenic challenge assays, we demonstrate that MRSA strains are resistant to ΦETA acquisition. All the 4/89 (4.5%) strains that were successfully lysogenized with ΦETA were characterized as methicillin-susceptible SA (MSSA). While lysogenic conversion did not modify other phenotypic markers, it increased the biofilm production, indicating potential fitness advantages conferred by ΦETA lysogenization. We also hypothesized that phage sequences in challenged strains may provide immunity against ΦETA, thus prophage presence and diversity may correlate with ΦETA susceptibility. Among the 89 strains tested, we bioinformatically identified that 54 of them contained at least one intact prophage sequence. Interestingly, all successfully lysogenized strains lacked intact prophages in their native state which contradicts the poly-lysogenic nature of SA. Additionally, the enhancement of biofilm formation after lysogenic conversion by ΦETA could be associated with pathogenesis of SSSS, increased invasiveness and even emergence of clinically relevant strains. Further studies are needed to explain the genetic and transcriptional basis of phenotypic changes. Together, our results underscore the vital role of ΦETA prophages in shaping SA diversity and clinical outcomes. This study highlights the necessity of investigating the molecular mechanisms associated with bacteriophage lysogenization and host range expansion.