Clostridium autoethanogenum is a gram-positive anaerobic bacterium that grows heterotrophically using fructose as a substrate, producing organic acids (formic, lactic, and acetic acid) and alcohols (ethanol and 2,3-butanediol). Literature reports show that electro-fermentation (EF) helps achieve higher production yields with Clostridium strains. EF involves manipulating microbial metabolism by applying an external potential using solid-state electrodes with/without redox mediators. However, the decrease in pH value can limit cellular viability and substrate conversion during the fermentation process. This work studies the effect of pH and neutral red as an electron transport on the kinetic of the growth and metabolites distribution during EF of C. autoethanogenum. Fermentation and EF experiments using C. autoethanogenum were performed in two-chamber H-type reactors. Biomass generation and product distribution were recorded in fermentations at pH 5.8 with and without pH control. As a result, when pH was controlled at 5.8, higher substrate consumption and biomass concentration were reached than when an external potential was applied (−600 mV vs. Ag/AgCl), allowing 76.6% more biomass with a 100% fructose conversion. Experiments revealed that redox mediator addition and the application of potential in pH-controlled fermentations mainly affected the production of biomass, lactate, acetate and formate, improving the production of lactate and acetate during the EF. In contrast, the results show no improvement in ethanol and 2,3-butanediol during the EF of fructose.