We describe a process configuration for the electrochemical acidification of milk using the desalination function and the acid/base production function of a bipolar membrane process. First, the milk is acidified by the acid produced in the bipolar membrane stack. The precipitate is removed by a solid/liquid separation. The supernatant whey is fed to the bipolar membrane stack for desalination. Next to desalination the stack is also used for acid and base production where the acid returns to the initial precipitation process and the base is used to neutralise the desalinated whey. Particular attention is paid to the discrimination of calcium scaling and protein fouling behaviour of different cation exchange membranes operating in the stack. Monovalent ion selective membranes show low scaling behaviour. The influence of different membrane configurations on the process efficiencies and the power consumption is tested. Current efficiency of the process suffers from proton leakage at anion exchange membranes. Using part of the casein whey to buffer the acid compartment process current efficiencies of 0.86 for the production of acid and 0.87 for the production of base can be achieved.