A high potential for modifying the texture properties of casein based dairy products through protein cross-linking by microbial transglutaminase (TG) has recently attracted considerable attention. Hereby, the impacts of different levels of TG and heat treatment of milk on the rennet gelation kinetics and microstructure properties of low-fat milk gel (~70% fat reduction) were investigated. The rheological analysis was measured by a dynamic rheometer and by a formagraph. In order to obtain complementary insights into the protein network formed, the gel microstructure was measured using confocal laser scanning microscopy. The results show that the influence of TG on the rennet coagulation properties appears more intense in the secondary phase measurable by; marked increase in curd yield percentages, intensive reduction in curd firmness, declined rigidity rate of casein network and markedly reduction in gel strength, than in the rennet primary phase represented in prolongation of the coagulation times.  A denser and more homogeneous systematic protein aggregate network accompanied by finer, smaller and evenly distributed pores, were observed in TG-treated gels. These effects on gelation kinetics and microstructure were more pronounced for higher TG concentrations and higher heat treatment of milk. A highly significant (P<0.001) and strong correlations were obtained among all formagraph and rheometer parameters. In sum, TG cross-linking intensely altered the functional properties of the resulting low-fat milk gel that might allow manifold applications and enhancement of low-fat cheese quality attributes.