When a mixed-culture microbial electrolysis cell (MEC) is fed with a fermentable substrate, such as glucose, a significant fraction of the substrate's electrons ends up as methane (CH4) through hydrogenotrophic methanogenesis, an outcome that is undesired. Here, we show that free ammonia-nitrogen (FAN, which is NH3) altered the glucose fermentation pathways in batch MECs, minimizing the production of H2, the "fuel" for hydrogenotrophic methanogens. Consequently, the Coulombic efficiency (CE) increased: 57% for 0.02 g of FAN/L of fed-MEC, compared to 76% for 0.18 g of FAN/L of fed-MECs and 62% for 0.37 g of FAN/L of fed-MECs. Increasing the FAN concentration was associated with the accumulation of higher organic acids (e.g., lactate, iso-butyrate, and propionate), which was accompanied by increasing relative abundances of phylotypes that are most closely related to anode respiration (Geobacteraceae), lactic-acid production (Lactobacillales), and syntrophic acetate oxidation (Clostridiaceae). Thus, the microbial community established syntrophic relationships among glucose fermenters, acetogens, and anode-respiring bacteria (ARB). The archaeal population of the MEC fed 0.02 g FAN/L was dominated by Methanobacterium, but 0.18 and 0.37 g FAN/L led to Methanobrevibacter becoming the most abundant species. Our results provide insight into a way to decrease CH4 production and increase CE using FAN to control the fermentation step, instead of inhibiting methanogens using expensive or toxic chemical inhibitors, such as 2-bromoethanesulfonic acid.