In this mini-review, the complexity of protein fractionation using ultrafiltration is discussed. The coupling of the system hydrodynamics, boundary layer transport, membrane permeation, electrostatic and hydrophobic interactions and its effects on protein transmission and membrane selectivity are analysed. Although ultrafiltration is promising for larger scale protein purification and also with outstanding advantages both technically and economically, much needs to be done to derive the general guidance for membrane selection, process design and system operation. With fine tuning of operational and physiochemical conditions, the process can be greatly improved in terms of process productivity and protein purity. A coupled multi-scale approach might provide a way forward to analyse this complex system and improve the confidence in applying such a promising technology and predictability of the outcome. In this mini-review, the complexity of protein fractionation using ultrafiltration is discussed. The coupling of the system hydrodynamics, boundary layer transport, membrane permeation, electrostatic and hydrophobic interactions and its effects on protein transmission and membrane selectivity. Although ultrafiltration is promising for larger scale protein purification and also with outstanding advantages both technically and economically, much needs to be done to derive the general guidance for membrane selection, process design and system operation. With fine tuning of operational and physiochemical conditions, the process can be greatly improved in terms of process productivity and protein purity. A coupled multi-scale approach might provide a way forward to analyze this complex system and improve the confidence in applying such a promising technology and predictability of the outcome.