Anaerobic fermentation of organic waste streams by mixed culture generates a mixture of short chain carboxylic acids. To avoid inhibitory effects of the acids or their consumption in internal conversion reactions in the mixed culture environment, in-situ recovery of acids can be beneficial. In this study, electrodialysis with bipolar membranes (EDBM) was applied to a mixed culture fermentation on organic waste streams using a novel EDBM stack with “direct contact” operation mode. We could demonstrate simultaneous recovery of carboxylates from the fermenter by the EDBM stack while in-situ generation and transport of hydroxyl ions to the fermenter allowed direct pH control. Experiments showed productivity increase after EDBM coupling to the fermenter, and complete elimination of external base consumption. It was also observed that EDBM was able to drive the mixed culture fermentation towards acetate and propionate type of carboxylates.