AbstractEnzymatic modifications of small molecules are a common phenomenon in natural product biosynthesis, leading to the production of diverse bioactive compounds. In polyketide biosynthesis, modifications commonly take place after the completion of the polyketide backbone assembly by the polyketide synthases and the mature products are released from the acyl‐carrier protein (ACP). However, exceptions to this rule appear to be widespread, as on‐line hydroxylation, methyl transfer, and cyclization during polyketide assembly process are common, particularly in trans‐AT PKS systems. Many of these modifications are catalyzed by specific domains within the modular PKS systems. However, several of the on‐line modifications are catalyzed by stand‐alone proteins. Those include the on‐line Baeyer‐Villiger oxidation, α‐hydroxylation, halogenation, epoxidation, and methyl esterification during polyketide assembly, dehydrogenation of ACP‐bound short fatty acids by acyl‐CoA dehydrogenase‐like enzymes, and glycosylation of ACP‐bound intermediates by discrete glycosyltransferase enzymes. This review article highlights some of these trans‐acting proteins that catalyze enzymatic modifications of ACP‐bound small molecules in natural product biosynthesis.