The effect of the addition of microbial TGase to milk on selected physical properties of the final product and the viability of lactic acid bacteria cultures during storage at 6 °C for 56 days was studied. Three types of set-style yogurt were made with varying parameters. Weekly analyses included the determination of syneresis and water-holding capacity, texture, pH, and the lactic acid bacteria population. Our research has confirmed that mTGase may be used to stabilize yogurts, although the syneresis, the water-holding capacity of yogurts, and the textural features of yogurts were dependent on the step in the production process at which mTGase was added to milk. The presence of mTGase had no relevance with regard to the acidity of yogurts stored under refrigerated conditions. The addition of mTGase had no effect on lactobacilli, but had a variable effect on Streptococcus thermophilus, depending on the duration of enzymatic activity.