To elucidate the catalytic mechanism of cobalt(III)–benzonitrile and iron(III)–-pivalonitrile hydratases, we have performed at density functional level a study using the cluster model approach. Computations were made in a protein framework. Following the suggestions given in a recent work on the analogous enzyme Fe(III)–NHase, we have explored the feasibility of a new working mechanism of examined enzymes. According to our results, after the formation of enzyme substrate complex, the reaction evolves toward product in only three steps. The first one is the nucleophilic attack, led by the −OH group of the αCys113–S–OH on the nitrile carbon atom, followed by the amide formation and by the enzyme restoring phase that our computations indicate as the most expensive step from the energetic point of view in both catalytic processes.