Membrane filtration, especially in combination with diafiltration, can affect the colloidal structure of casein micelles in milk and concentrated milks. The partial dissociation of casein proteins from the casein micelles into the serum phase has been shown to depend on diafiltration conditions. This dissociation can affect the technological functionality of the milk concentrates. The present study aimed at determining the contribution of the gel layer deposited onto the membrane during filtration in the colloidal equilibrium between soluble and micellar caseins. Skimmed milk was concentrated by microfiltration combined with diafiltration using a cross-flow spiral-wound membrane at two transmembrane pressure (TMP) levels, causing differences in the extent of the gel layer formed. Non-sedimentable casein aggregates were formed to a greater extent at a low TMP compared to a high operating TMP. This difference was attributed to the greater compression of the deposit layer during filtration at a high TMP. This study contributes new knowledge to the understanding of how to modulate the functionality of milk concentrates through the control of processing conditions.