Moderate and high humidity cheeses are described as important vehicles of pathogens in many foodborne diseases outbreaks. Microbial contamination can occur in raw material or in the different steps of the product processing due to inadequate hygiene practices. Thus, the aim of this study was to evaluate the microbiological quality and safety in the production of moderate and high humidity cheese. Samples from raw milk, handlers’ hands surface, final product were collected in three cheese manufacturing plants located in southern Brazil, with different levels of sanitary control. Effectiveness of milk pasteurization was also evaluated. Thermotolerant coliforms, coagulase-positive staphylococci (CPS), Salmonella spp., and Listeria monocytogenes were evaluated. Raw milk samples showed the highest contamination levels, with enumeration of 1.1x105 most probable number (MPN) mL-1 for thermotolerant coliforms, 4x105 colony-forming units (CFU) mL-1 for CPS and presence of Salmonella spp. CPS were also reported in one sample of handler’s hands surface. However, only one sample of the final product was out of Brazilian regulatory standards, exceeding the limit allowed for CPS. Milk pasteurization process used in cheese preparation was effective, regardless the level of sanitary control of the industries. Results highlighted the need for better hygiene practices, in obtaining the raw milk and in the handling during the cheese manufacturing steps.