Membrane fouling by proteins is an important problem in hemodialysis or hemofiltration (artificial kidney). The mechanisms leading to fouling are still not fully understood and then predictable. In this paper we describe a microfluidic chip fitted with a filtration membrane which allows the real time in situ fluorescent analysis of labelled proteins and the measurement of the membrane permeability. The apparent kinetics rates of adsorption derived from the changes in fluorescence signal are combined with permeability measurements. This allows to discriminate two clearly distinct fouling mechanism by Bovine Serum Albumin (BSA) and α-lactalbumin (LALBA). The fouling kinetics of BSA is very rapid, independent of the flow conditions and can then be viewed as a protein monolayer adsorption controlled by protein-membrane interactions. In contrast, the fouling kinetics by LALBA is slower and very sensitive to flow conditions. We also describe a fluorescence quenching induced by protein aggregation and compression at high permeation rate. The fouling mechanism can then be viewed as a flow induced aggregation followed by a deposition of aggregates on the membrane. The complexity of sorption mechanisms on membrane during cross-flow filtration can be unraveled with this experimental set-up.