S. aureus is a human pathogen that is extremely adaptable and is the cause of a variety of nosocomial and community-acquired infectious illnesses. During infection, S. aureus affect the host cell in many ways to enable its own multiplication, spread, and evasion of host immune defense. One of S. aureus mechanism to survive is to inhibit the SUMOylation of host proteins in order to increase its intracellular survival and persistence for longer period of time. Here, we show that the reduction in the levels of cellular SUMO-conjugated proteins is associated to the PtpA secreted virulence factor, which results in a reduction of Ubc9 protein level, the essential enzyme of the SUMOylation modification. In addition, we demonstrated that the critical residue D120A, essential for PtpA phosphatase activity, is required. This study shows for the first time that the secreted phosphatase PtpA impedes the host SUMOylation response, thus promoting S. aureus survival at long-term infection.