During the production of organic acids, ion-exchange is currently the first choice for acidifying organic salts. However, when it comes to environmental benignity and technological advances, electrodialysis with bipolar membranes (EDBM) is preferable. To determine which one is the more competitive, this research chooses gluconic acid as a model organic acid and performs a theoretical calculation of process cost by introducing two factors for environmental pollution and bipolar membrane prices. Results indicate that, currently, the total process cost for ion-exchange is $0.057kg −1 and less than that for EDBM ($0.085–0.407kg −1 ). However, when the environmental factor and the membrane factor are both considered (between 0.21 and 0.76), the best strategy for acidifying gluconate is to integrate EDBM and ion-exchange. Naturally, EDBM will have more competence as a role of environmental cost increases and bipolar membrane prices decrease.