Potato fruit juice as a by-product of the starch industry contains proteins with interesting functionalities such as protease inhibitors or patatin with its high nutritional value. Due to their functional properties, these proteins are principally of industrial interest. A drawback for the application of these potato proteins is the separation and isolation under maintenance of the biological activity. So far, there are no methods in literature, which are satisfying concerning the costs or the separation performance. In this study, we show a chromatographic approach using natural clay minerals as cation exchangers to separate two protein fractions in potato fruit juice. Additionally, the content of glycoalkaloids naturally occurring in potatoes is significantly reduced in a single step together with the separation of the patatins and the protease inhibitors.