The application of bipolar electrodialysis (BPED) for the simultaneous removal of inhibitory acetate and pH control during E. coli fermentation was investigated. A two cell pair electrodialysis module, consisting of cation exchange, anion exchange and bipolar membranes with working area of 100 cm2 each, was integrated with a standard 7 l stirred tank bioreactor. Results showed that BPED was beneficial in terms of in situ removal of inhibitory acetate and a reduction in the amount NH4OH used for pH control. In batch and fed-batch BPED fermentations, base additions were decreased by up to 50% in both cases compared to electrodialysis (ED) fermentations with pH controlled at 6.7 ± 0.1. Consequently, the final biomass (34.2 g DCW l−1) and recombinant protein (5.5 g l−1) concentrations obtained were increased by up to 37 and 20%, respectively.