Milk protein concentrates (MPC) are widespread food ingredients, due to their high protein-to-solids ratio, nutritional value, and technological properties, which can be tailored to various end uses. Interest has been given to modifying such ingredients through enzymatic cross-linking by microbial transglutaminase. However, no systematic studies on the cross-linking kinetics of casein micelles at different concentration factors are currently available, although the enzyme might act in a considerably different fashion at decreased inter-particle distances. In this study, cross-linking of casein micelles was studied in a 4x MPC obtained by ultrafiltration, and compared to that of the original skim milk. The cross-linking kinetics were evaluated by following the degree of casein polymerisation using size exclusion chromatography. The extent of polymerisation for both skim milk and 4x MPC could be scaled to a master curve by normalising the incubation time to concentration factor and enzyme level, indicating similar cross-linking kinetics. Likewise, the cross-linking of individual casein types followed the same trend regardless of treatment. However, the casein micelle size increased with cross-linking at 4x but decreased at 1x concentration, suggesting enhanced cross-linking on the surface of the casein micelles in MPC suspensions. These results are relevant for the design of novel milk protein ingredients.