Enzymatic cross-linking by microbial transglutaminase is a prominent approach to modify the structure and techno-functional properties of food proteins such as casein. However, some of the factors that influence structure-function-interrelations are still unknown. In this study, the size of cross-linked sodium caseinate nanoparticles was modulated by varying the ionic milieu during incubation with the enzyme. As was revealed by size exclusion chromatography, cross-linking at higher ionic strength resulted in larger casein particles. These formed acid-induced gels with higher stiffness and lower susceptibility to forced syneresis compared to those where the same number of ions was added after the cross-linking process. The results show that variations of the ionic milieu during enzymatic cross-linking of casein can be helpful to obtain specific modifications of its molecular structure and certain techno-functional properties. Such knowledge is crucial for the design of protein ingredients with targeted structure and techno-functionality.