Transglutaminase enzyme is proven to improve some of food and beverages' characteristics by creating a cross-linking process between food protein molecules. This study was conducted to evaluate the effect of cross-linked milk protein caused by transglutaminase addition on conductivity and functional properties of yogurt such as sensory & microstructural properties, protein content, and electrophoresis profile. Transglutaminase enzyme was added at concentration of 1 UE/gram milk protein at two different manufacturing steps, those are before addition of lactic acid bacteria and concomitant with lactic acid bacteria addition. Samples were analyzed at 1, 8, and 15 days storage period. The result showed that the conductivity of samples increased during fermentation process, with the conductivity of the transglutaminase-treated sample tended to increase slower than that of the non-treated sample. Sensory analysis of samples showed that transglutaminase addition had no significant effect on the samples' aroma and taste, but it caused a noticeable effect on samples' consistency and physical appearance. This enzyme activity was shown to have significant effect on protein content of samples which was increasing during storage period, with more significant result for sample with transglutaminase addition simultaneously with lactic acid bacteria addition. Based on the results of electrophoresis analysis, transglutaminase led to formation of bigger protein molecule due to cross-linking process, causing the more compact of protein network in yogurt. It can be concluded that transglutaminase can be used effectively to improve yogurt properties.