Caseinate dissolved in different ionic milieus was used as model substrate for cross-linking by microbial transglutaminase and subsequent acid-induced gelation. The study follows up on previous research, where the molecular properties of cross-linked casein nanoparticles were linked to certain rheological characteristics of acid gels (Raak et al., 2019, Food Hydrocoll 86:43–49), and presents additional insight into physical gel properties. The frequency dependency of the storage modulus followed a power law relationship, with the exponent being linearly related to the phase angle. The frequency dependency of the loss factor could be fitted with a second-order polynomial function, the minimum of which was shifted to lower frequency at increasing cross-linking extent. Strain sweep experiments showed a less pronounced strain hardening behaviour and reduced fracture strain with increasing cross-linking extent, indicating lower flexibility of cross-linked casein nanoparticles and a lower number of non-covalent bonds, respectively. The water holding capacities of the gels were in a good relationship with the fracture properties, suggesting that the serum drainage during centrifugation was also affected by the strain hardening behaviour. Additionally, diffusing wave spectroscopy showed that the casein particles interacted already prior to the gelation onset, and that the presence of Ca²⁺ ions increases the particle size in both the caseinate solutions and gels