Microbial transglutaminase (MTGase) is an enzyme widely used in the dairy sector to improve the functional properties of protein-based products via the formation of a network between protein molecules. The aim of this study involving cheese from the milk of donkeys was to evaluate the effects of treatment with MTGase at the concentrations of 0 (control), 5, 8 and 10 U/g milk protein on the cheese-making process parameters, as well as the physical and chemical characteristics of the resulting cheese. MTGase influenced the time of gel formation from rennet addition (P < 0.05), with a delay at the two highest concentrations, accompanied by a lower (P < 0.01) pH of cheese and the lowest (P < 0.01) loss in cheese weight at 24 h of storage. The highest gel viscosity (P < 0.01) was observed at the highest concentration of the enzyme, reaching the value of 70 mPa⋅sec after 60 min. The chemical composition and color of the cheeses were not significantly affected by the inclusion of MTGase, regardless of the enzyme concentration. These findings may be of relevance in adapting the cheese-making process and might help in the design of new dairy products from donkey's milk.