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This study investigated the presence of nontuberculous mycobacteria (NTM) for the first time in two types of unpasteurized fresh cheese produced in the state of Michoacan, Mexico. We tested for this pathogen, along with the others, to broaden the study of microbiological quality in 60 samples of cheese, 30 fresh and 30 Adobera, which were collected from six artisanal cheese factories (ACFs). The hygienic conditions of these establishments and the practices of cheese manufacture were generally poor. Although Mycobacterium boviswas not detected, four cheese samples harbored NTM isolates. The four NTM isolates were identified using three molecular markers (hsp65, rrs,and rpoBgenes) that corresponded to Mycolicibacterium fortuitum(n= 3) and Mycolicibacterium mageritense(n= 1). All 60 cheese samples analyzed had unsatisfactory microbiological quality according to the Mexican Official Guideline. Regarding fresh cheeses, all 30 samples analyzed were positive for aerobic mesophilic bacteria, total coliforms, fecal coliforms, and yeasts and molds. Escherichia coliand Staphylococcus aureuswere present in 23 and 21 samples, respectively. Listeria monocytogeneswas identified in a sample and was isolated from a bulk milk tank in the same ACF. With regard to Adobera cheeses, all samples were positive for aerobic mesophilic bacteria, total coliforms, fecal coliforms, yeasts and molds, and S. aureus. E. coliwas isolated from 28 samples. Salmonellawas isolated from a sample and from a wooden shovel used in the manufacture of the cheeses in the same ACF. Thus, the consumption of unpasteurized fresh cheese may represent a public health risk. Because of this, health authorities should enforce the legislation that forbids the processing of cheese with unpasteurized milk and encourage producers to follow good manufacturing practices from original ingredients, through the production process of the cheese, to its sale to assure a safe product.