The integrated electrodialysis (ED) process supports valorisation of a lactose-rich side stream from the dairy industry, creating an important source of milk sugar used in various branches of the industry. This work focuses on the optimization of the downstream processes before the crystallization of lactose. The process line includes a pre-treatment and desalination by ED of the industrial waste solution of the lactose mother liquor (LML). The LML was diluted to 25% total solids to overcome hydraulic issues with the ED desalination process. Two different levels of electrical conductivity reduction (70% and 90%) of the LML solutions were applied to decrease the mineral components and organic acids of the LML samples. The ED performance parameters such as ash transfer rate (J), the specific capacity (C_F) of the ED and specific electric energy consumption (E) were determined and the influence of the LML solution on the monopolar ion-exchange membranes has been investigated. A higher degree of desalination is associated with higher electric energy consumption (by 50%) and lower specific capacity (by 40%). A noticeable decrease (by 12.8%) in the resistance of the anion exchange membranes was measured after the trials whereas the resistance of the cation exchange membranes remained practically unchanged. Any deposition of the alkaline earth metals on the membrane surface was not observed.