Artisanal cheeses bearing the ARTE seal are authorized for nationwide commercialization and are produced in accordance with quality standards established by specific regulations. In contrast, cheeses without this certification have their sale restricted to municipal or state-level commerce, subject to registration with official inspection services. This study evaluated the microbiological quality of Minas artisanal cheeses produced in the Serra da Canastra region, Minas Gerais, by comparing products from farms with and without the ARTE seal. A total of 69 samples were analyzed, including raw milk, pasteurized milk, curd, cheese, and swabs from cheese molds, collected from 16 farms, eight certified with the ARTE seal and eight uncertified. Microbiological quantification techniques, culture methods, and polymerase chain reaction (PCR) assays were employed for pathogen identification, alongside phenotypic antimicrobial susceptibility testing and genetic similarity analysis of Staphylococcus aureus isolates via pulsed-field gel electrophoresis (PFGE). Neither Salmonella spp. nor Listeria monocytogenes were detected. Elevated counts of Enterobacteriaceae and coagulase-positive staphylococci were more frequently observed in ARTE-certified farms; however, Staphylococcus aureus was isolated exclusively from uncertified properties. These findings suggest that the ARTE seal may contribute to more effective sanitary practices and enhanced microbiological safety of artisanal cheeses.