This study assessed the microbiological quality and safety of mozzarella during various production stages in northern Tocantins, Brazil, by identifying critical biological points in the industrial environment within a tropical climatic region. Batches of mozzarella were evaluated, from raw milk to primary packaging, with a shelf life of 120 d at 4°C. Indicator microorganisms were quantified, and through microbiological and biomolecular approaches, Salmonella spp. and Listeria monocytogenes were identified. In addition, the toxigenic potential of coagulase-positive staphylococci (CPS) was characterized. Results indicated that the raw milk used for mozzarella production had low microbiological quality; pasteurization of raw milk effectively eliminated all identified pathogens and reduced microbiological counts (p > 0.05). An increase in bacterial counts (>2 log colony-forming unit [CFU]/g) and recontamination with Salmonella spp. and CPS, which potentially produce staphylococcal enterotoxin B, were observed during milk coagulation and curd draining. Stretching of the fermented curd reduced the enterobacteria, total coliforms, and Escherichia coli median values by 2.56, 2.64, and 2.3 log CFU/mL, respectively. Similarly, brining the pieces by immersion reduced the quantity of enterobacteria and total coliforms by 2.3 and 1.6 log CFU/mL, respectively. Of interest, in the freshly finished product, Salmonella spp. was present but L. monocytogenes was absent; however, after the shelf-life period, L. monocytogenes was present but Salmonella spp. was absent. Considering the environmental conditions that can promote the multiplication and preservation of pathogens and spoilage of dairy products in tropical climates, it is necessary to review operational hygiene procedures, particularly in milk coagulation vats and fermentation tables. This will ensure the production of high-quality mozzarella cheese with a reduced consumption risk.