Minas Frescal cheese is a typical Brazilian cheese with a white and soft appearance and no ripening. Probiotics are live microorganisms, which confer health effects to the host when administered in adequate amounts. This study aimed to evaluate the impact of modified atmosphere packaging on the quality parameters of Minas Frescal cheese added with Bifidobacterium animalis ssp. lactis (6 log CFU/g). Five different packaging flexible nylon/LDPE packaging were evaluated: (CONT) atmospheric air, (CO2) 100% CO2, (N2) 100% N2, (CO2-N2) 50% CO2/50% N2, and (VAC) vacuum. The cheeses were analyzed for packaging evaluation, organic acid content (acetic, lactic, and citric acid), and rheological properties (texture profile analysis, uniaxial compression, and creep analysis) during storage (28 days). Data were submitted to the Analysis of Variance (ANOVA) and Tukey test (p < 0.05). The flexible nylon/LDPE packaging showed a thickness of 48.50 ± 1.66 µm and oxygen permeability rate (TPO2) of 45.38 ± 1.05 cm³ (CNTP)/(m2.day) at 23 °C and 50% moisture. The vacuum packaging (VAC) showed no O2 and CO2 concentrations throughout the entire storage period. The CONT sample showed approximately 21% of O2 at day 1. In this package, the O2 concentrations decreased, and the CO2 concentrations increased during storage. The CO2 package had 100% CO2 at day 1, but no CO2 was observed after 7 days of storage, resulting in a vacuum environment. The N2 package had no O2 and CO2 concentrations at day 1, but the CO2 concentration increased during storage. The lactic acid content was higher in the MAP stored cheeses (N2, CO2, CO2-N2, and VAC) compared to CONT. MAP utilization did not alter the acetic acid concentration and rheological properties of the products (p > 0.05). CO2 and VAC cheeses showed similar characteristics for the evaluated parameters, while N2 and CO2-N2 cheeses showed higher lactic acid content.