Pretreatment of whey by microfiltration (MF) has emerged as a necessary step in producing high purity whey protein concentrates. In the MF of pretreated whey using a Carbosep M14 membrane (pore diameter 0.14 μm), proteins and calcium phosphate aggregates were responsible for fouling, which increased according to the “complete blocking” filtration law and accounted for a progressive decrease of the active filtering area. An operating mode with dynamic counter pressure (recirculation of the permeate co-current to the retentate), as opposed to static counter pressure, allowed lower overall fouling, a longer time of operation and better protein recovery because of more evenly distributed fouling along the membrane tube. At shorter times of operation, fouling was greater under higher transmembrane pressure (TP), so that the less fouled areas under lower TP were forced to filter larger volumes and consequently became fouled more rapidly. This involved a movement of the effective filtering area along the membrane tube, as evidenced by the systematic evolution of fouling heterogeneity as measured by infra-red spectroscopy.