The main objectives of the present study were to determine the occurrence of coagulase positive staphylococci (CPS) and to assess the presence and antimicrobial susceptibility profile of Staphylococcus aureus isolates in different raw milk origin (cow and sheep) traditional cheeses marketed in Banat region, Romania. Additionally, the presence of mecA gene in S. aureus isolates and the staphylococcal enterotoxins (SEs) in cheese samples were evaluated. A total of 81.6% (138/169) of the screened samples were positive for CPS. Furthermore, 35.5% (49/138) of the investigated CPS positive cheese samples were contaminated with S. aureus, with an isolation frequency of 46.6% (14/30) in caș, 33.3% (32/96) in telemea, 25% (2/8) in burduf, and 25% (1/4) in urdă assortments, respectively. From the total number of S. aureus isolates, 6.1% (3/49) harbored the mecA gene. Detectable levels of SEs were identified in 4.3% (4/94) of cheese samples with a CPS contamination level higher than 105 log CFU g−1. The expressed antimicrobial susceptibility profile of the tested cheese-origin S. aureus isolates, with the automated Vitek 2 equipment, showed resistance towards amikacin (90.1%, 10 out from 11 tested), enrofloxacin (86.2%, 25/29), ceftiofur (72.7%, 8/11), neomycin (63.6%, 7/11), benzylpenicillin (53.1%, 26/49), kanamycin (41.4%, 12/29), rifampicin (39.5%, 15/38), tetracycline (38.8%, 19/49), tilmicosin (36.4%, 4/11), clindamycin (30.6%, 15/49), ciprofloxacin (30%, 6/20), erythromycin (22.4%, 11/49), tylosin (18.2%, 2/11), oxacillin (16.3%, 8/49), linezolid (15%, 3/20), teicoplanin (15%, 3/20), fusidic acid (13.1%), imipenem (10.5%, 4/38), vancomycin (7.9%, 3/38), ampicillin (5.5%, 1/18), mupirocin (5.5%, 1/18), fosfomycin (5%, 1/20), and gentamicin (4.1%, 2/49). Twenty-four (49%) S. aureus isolates exhibited multidrug resistance. The investigation highlighted a common occurrence of multidrug-resistant S. aureus strains in the monitored cheese assortments, which can constitute a potential risk for consumers’ health.