The physical and chemical changes of 4x milk concentrates prepared by ultrafiltration (UF) and microfiltration (MF) combined with diafiltration were studied after heating in situ to 85 °C and subsequent cooling. Skim milk (1x) was analyzed as control. The concentrates had comparable pH, colloidal casein and colloidal calcium and phosphate, but differed in whey proteins and serum calcium and phosphate, allowing investigating the effect of soluble phase composition on viscosity changes and protein aggregation during heating. In heated samples, there was a decrease in the apparent diameter of the protein particles, as well as a decrease in bulk viscosity compared to unheated concentrates. On the other hand, the turbidity increased. Particles’ diffusivity measured by diffusive wave spectroscopy was slower in UF concentrate compared to the MF counterpart, both before and after heating, demonstrating the effect of protein aggregates in the soluble phase in changing the bulk properties of the concentrates. In this work, by comparing 4x MF and UF fresh concentrates with reduced calcium, and with similar processing history, it was demonstrated that the presence of whey proteins drives casein dissociation. MF concentrates showed increased heat stability compared to UF concentrates, with lower viscosity after heating. It was also observed that cooling kinetics affect the dissociation of caseins in heated skim milk. A fine control of diafiltration for ions and whey protein depletion is critical for control of the technological quality of the concentrates.