Fouling of microfiltration membranes leads to severe flux declines and the need to clean or replace the membrane. In situ 3D characterization of protein fouling both on the surface and within the pores of the membrane was achieved using multiphoton microscopy. Time-lapse images of the fouled membrane were obtained for single suspensions and mixtures of fluorescently labeled bovine serum albumin and ovalbumin. Deposited protein aggregates were visible on the membrane and evidently play an important role in fouling. A combination of 3D images and resistance versus time data was used to identify the dominant fouling mechanism. Fouling is initially internally dominated, but after 1 and 15 min for ovalbumin and bovine serum albumin, respectively, the fouling becomes externally dominated. This is in good agreement with two-stage protein fouling models.