Probiotics are live microorganisms that, when administered in adequate amounts, confer health benefits on the host. For this reason, the viability and metabolic activity of these microorganisms must be maintained at all stages of food processing, from manufacture to ingestion by the consumer. Furthermore, they must be able to survive conditions in the human gastrointestinal tract. Since Bifidobacterium animalis is a strictly anaerobic bacterium, its use in probiotic foods becomes a challenge. Thus, packaging systems that prevent the bacteria from coming into contact with oxygen may represent an alternative. This work aimed to evaluate the viability of the probiotic culture Bifidobacterium animalis subsp. lactis (BB-12®, CHR Hansen) after refrigerated storage of Minas Frescal cheese conditioned in CO2, N2, and vacuum atmospheres. At intervals of 1, 7, 14, and 21 days, microbiological analyses were carried out for selective counting of the probiotic bacteria and evaluating their viability when subjected to conditions in the gastrointestinal tract. In addition, the quantification of metabolic compounds (acetic, lactic, and citric acid) by HPLC was also performed. Cheeses packaged in modified atmosphere and vacuum packaging systems showed higher counts of bifidobacteria and, consequently, higher acetic acid concentrations, demonstrating their metabolic activity. Therefore, we can state that packages with internal oxygen suppression and materials with a high gas barrier and adequate sealing to maintain anaerobiosis should represent an essential component to be considered by the probiotic food industry, regardless of the type of treatment applied.