The neutralization of milk whey after the electrodialysis (ED) is usually carried out by direct addition of NaOH or KOH solution. However, the addition of these solutions results in an increase in total solids and ash content of the whey sample. In this work, electrodialysis with the bipolar membrane (EDBM) was examined to neutralize the desalinated whey after ED. First, ED was used to desalinate the nanofiltrated whey (NFW). Three milk whey samples differing in demineralization rate in ED were subjected to the EDBM. Two configurations of EDBM were applied to increase the pH of the milk whey samples. When the samples which had been demineralized first with conventional ED, were submitted in EDBM the pH increased to the desired values. However, the pH of NFW sample only increased to the values less than 6. The changes in pH, total solids, ash content, and minerals profile of various samples after EDBM were investigated. It was figured out that the increase in pH was not accompanied by any significant increase in total solids and ash content of the samples. The mechanisms of ion transport during EDBM for either cations or anions were investigated. The cations were mainly transported by diffusion in developed configurations of EDBM while anions were transported either with diffusion or migration depending on the type of milk whey sample. With increasing the demineralization rate of the whey in ED the diffusional transport of species in EDBM reduces due to the decrease in ion content of the whey. Two configurations of EDBM were compared in terms of fouling on the BM surface, electrodialysis capacity, and energy consumption.