Desalination of nanofiltrated acid whey by electrodialysis in the temperature range 15–55 °C was investigated. Increased electrodialysis temperature caused increased total mass flux and electrodialysis capacity while specific energy consumption values were maintained. Weak organic acids removal from whey increased with temperature, leading to an increase in the degree of deacidification from 64.3% to 72.0% when the temperature increased from 15 to 55 °C. Protein losses were not observed at any temperature, and the increase in ED temperature did not affect the protein content of the desalted whey. IR spectroscopy showed that protein deposition occurred mainly in the surface layers of cation-exchange membranes. Conductivity and diffusion permeability of anion-exchange membranes increased after electrodialysis at elevated temperatures due to the enlargement of pores and channels of ion-exchange materials. Protein sorption by cation-exchange membranes significantly compensated for this effect and their transport properties changed to a much lesser extent.