Microbial transglutaminase (mTGase) is a known enzyme capable of modifying the structure of proteins through the formation of cross-linking, resulting in protein polymerisation. Milk proteins are an excellent substrate for mTGase cross-linking. The cross-linking formation is related to the environmental conditions of incubation, including pH, temperature, protein concentration, enzyme concentration, and mineral or reducing agents addition; thus, it is vital to better understand the leverages for the protein cross-linking. To elucidate how these leverages affect the cross-linking reaction, the current state of knowledge concerning the impact of environmental conditions on the enzymatic cross-linking between milk proteins was scouted. The potential applications of mTGase cross-linked dairy proteins on food products such as cross-linked milk powders, protein beverages, processed cheese, ice cream, encapsulation of bioactive compounds, and edible films are described. Additionally, the patents addressing the functionalisation of milk products through enzymatic modification are reported.