Milk protein fractionation by microfiltration membranes is an established but still growing field in dairy technology. Even under cross-flow conditions, this filtration process is impaired by the formation of a deposit by the retained protein fraction, mainly casein micelles. Due to deposition formation and consequently increased overall filtration resistance, the mass flow of the smaller whey protein fraction declines within the first few minutes of filtration. Currently, there are only a handful of analytical techniques available for the direct observation of deposit formation with opaque feed media and membranes. Here, we report on the ongoing development of a non-invasive and non-destructive method based on magnetic resonance imaging (MRI), and its application to characterise deposit layer formation during milk protein fractionation in ceramic hollow fibre membranes as a function of filtration pressure and temperature, temporally and spatially resolved. In addition, the chemical composition of the deposit was analysed by reversed phase high pressure liquid chromatography (RP-HPLC). We correlate the structural information gained by in-situ MRI with the protein amount and composition of the deposit layer obtained by RP-HPLC. ... mehrWe show that the combination of in-situ MRI and chemical analysis by RP-HPLC has the potential to allow for a better scientific understanding of the pressure and temperature dependence of deposit layer formation.