The transition towards a carbon-neutral society necessitates radical approaches in the bio-refinery pipeline, particularly in the production of organic acids. The current downstream process from a dilute fermentation broth is limited by the extensive use of acids and bases, along with heavy reliance on energy-intensive distillation. In this work, we propose an entirely membrane-based process to purify organic acids (e.g., gluconic acid) from a crude solution of catalytic dehydrogenation of glucose. To facilitate downstream purification, we introduce an innovative membrane-assisted ion exchange (MEM-IE) strategy, which is a scalable process that can protonate ionic compounds entirely in the solution phase. Instead of a solid ion exchange resin, a bulky yet soluble acidification agent is used to protonate the target compound, which can be easily separated via a size exclusion membrane. We selected non-toxic poly (4-styrene sulfonic acid) (H-PSS, 75 kDa) as the acidification agent to selectively protonate gluconate ions and to enable facile fractionation. The proposed MEM-IE strategy can overcome the scale-up limitation of traditional solid ion exchange resins and can be applied to many types of ionic compounds. The versatility of the proposed process was also demonstrated on formate and lactate compounds. A techno-economic evaluation using the Verberne cost model showed that the proposed process achieves an 80 % reduction in energy consumption compared to the fermentation-based process, and the return on investment (ROI) of a 330 ton-per-day plant was less than a year. The proposed membrane-based process for the purification of organic acids, particularly the MEM-IE strategy, offers a sustainable and energy-efficient downstream separation platform.