Abstract The aim of this work was to study the effect of the concentrate solution pH and the composition in calcium, carbonate and protein of the diluate solution to be treated by conventional electrodialysis on the fouling of ion-exchange membranes. Conductivity, system resistance, pH of the diluate and cation migration were monitored to follow the evolution of the demineralization. Total cation migration was similar for all conditions although different forms of fouling were identified after three consecutive 100 min electrodialysis treatments. The nature of fouling and the membrane surface fouled depended on the concentrate pH value, the diluate mineral composition and the intrinsic composition of the whey isolate. Once conditions leading to membrane fouling were identified, an alternative configuration for our electrodialysis stack is proposed to prevent fouling onset.