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In this study, milk protein isolate (MPI) and micellar casein concentrate (MCC) were obtained with ultrafiltration (UF) and microfiltration (MF), respectively. The objective of this work was to evaluate the effect of diafiltration (DF), the addition of water during filtration, on the colloidal dissociation of casein micelles. Two levels of DF were applied after an initial concentration step to 2x the volume fraction, at a total protein concentration of about 7% (w/v). Under these conditions, while permeation of protein was still measured in the permeates, calcium ion transmission reached a plateau. The molecular details of the serum phases were studied throughout the filtration process. A comparison of serum phases with and without whey protein (UF vs MF) was carried out by examining the two processes in parallel, applying similar filtration conditions. Final 4x concentrates (based on initial volume of milk) were also compared. Viscosity was higher for UF than the corresponding MF concentrates, is spite of the higher level of colloidal protein present in the MF concentrates, which would suggest a change in the hydration or the volume/weight ratio (voluminosity) of casein micelles in MCC retentates. Centrifugal supernatants contained casein proteins both in MPC and MCC retentates. There were no statistically significant changes in the apparent hydrodynamic diameter of the casein micelles when measured by dynamic light scattering, in the original milk serum. A two dimensional chromatography was carried out on the soluble aggregates to determine differences in the amount of individual caseins. The aggregates showed only traces of whey proteins. The composition of the final concentrates, albeit similar in total proteins, showed profound differences in ionic strength and soluble proteins, suggesting that these parameters may be used as an indication of ingredient quality and functionality.