[en] Highlights: • A unitary mechanism for the cyclization of tetraketides in stilbene and chalcone synthase. • The identification of an active water that functions as a “Claisen switch” in chalcone synthase. • QM-MM and FMO analysis of model tetraketide ligands highlighting common and disparate components of binding pockets and cyclization sites in stilbene and chalcone synthase. The polyketide synthases found in a variety of plants and fungi provide a varied source of biologically active compounds of pharmacological and medicinal interest. Stilbene synthase and chalcone synthase catalyze the formation of a common tetraketide intermediate, but use different cyclization mechanisms to produce distinct and separate natural products. While key structural differences have been identified to explain this functional diversity, a fuller explication of the factors responsible for this mechanistic disparity is required. Based on the energetics of our models of the bound tetraketides, and our structural analysis of the active sites we propose that a key tautomeric conversion provides a mechanistic framework common to both cyclizations. A previously unidentified active water molecule facilitates cyclization in chalcone synthase through a Claisen mechanism. Such a “Claisen switch” is comparable to the previously characterized “aldol switch” mechanism proposed for the biosynthesis of resveratrol in stilbene synthase.