Despite the beneficial health effects of fruit juices, the high content of organic acids and low pH of some of them limit their consumption. The aim of this work was to study the deacidification of fruit juices using electrodialysis (ED) with monopolar membranes. Aqueous solutions of citric acid were used in ED deacidification experiments following a factorial design with citric acid concentration and electric current varying in the ranges of 5–25 g/L and 0.5–1 A, respectively. The design runs were characterized by a constant Faraday efficiency of 0.37 ± 0.03, suggesting that the triple-charged citrate ion (Cit3−) carried the electric charge through the anionic membranes. During deacidification, the pH increased in agreement with the decreasing concentration of the acid. Deacidification of pineapple juice or pineapple juice enriched with 20 g/L of citric acid using ED led to similar values of the Faraday efficiency, confirming that Cit3− is the main ion migrating through the anionic membrane. However, the decrease in titratable acidity during ED treatment was accompanied by a decrease in pH. Such behavior, already reported, was explained by considering proton generation during the transformation of the single (H2Cit−) and double-charged (HCit2−) citrate ions into the triple-charged ion (Cit3−) when entering the anionic membrane.