To evaluate the behaviour of the relevant microbial populations during stretched cheese production, the quantitative microbiological analysis was performed during the critical steps of the preparation. The obtained data distributions proved statistically significant increases in all indicators, on average by 4.55 ± 0.64 log CFU/g of presumptive lactococci counts, 4.06 ±0.61 of lactobacilli, 1.53 ± 0.57 log CFU/g of coliforms, 2.42 ± 0.67 log CFU/g of Escherichia coli, 1.53 ± 0.75 log CFU/g of yeasts and moulds, and 0.99 ± 0.27 log CFU/g of presumptive Staphylococcus aureus, from the early stage of milk coagulation until curd ripening (0–24 h). The following steaming/stretching process caused reductions in viable counts with the most significant inactivation effect on coliform bacteria, including E. coli (-4.0 ± 1.0 log CFU/g). Total viable counts and yeasts and moulds showed 2 and almost 3 log reduction (-2.2 ± 1.1 log CFU/g and -2.6 ± 0.9 log CFU/g), respectively. The lowest decreases in presumptive S. aureus counts were estimated at the level of -1.50 ± 0.64 log CFU/g. The counts of yeasts and moulds showed the best indicatory function during the entire storage period of vacuum-packaged cheeses at 6 °C.