Beta-amino acids are widely used building blocks in both natural and synthetic compounds. Aromatic beta-amino acids can be biosynthesized directly from proteinogenic alpha-amino acids by the action of MIO (4-methylideneimidazole-5-one)-based aminomutase enzymes. The uncommon cofactor MIO plays a role in both ammonia lyases and 2,3-aminomutases; however, the precise mechanism of the cofactor has not been resolved. Here we provide evidence that the electrophilic cofactor uses covalent catalysis through the substrate amine to direct the elimination and subsequent readdition of ammonia. A mechanism-based inhibitor was synthesized and the X-ray cocomplex structure was determined to 2.0 A resolution. The inhibitor halts the chemistry of the reverse reaction, providing a stable complex that establishes the mode of substrate binding and the importance of tyrosine 63 in the chemistry. The proposed mechanism is consistent with the biochemistry of aminomutases and ammonia lyases and provides strong support for an amine-adduct mechanism of catalysis for this enzyme class.