<jats:title>Abstract</jats:title><jats:p>The antibiotic kirromycin is assembled by a hybrid modular polyketide synthases (PKSs)/nonribosomal peptide synthetases (NRPSs). Five of six PKSs of this complex assembly line do not have acyltransferase (AT) and have to recruit this activity from discrete AT enzymes. Here, we show that KirCI is a discrete AT which is involved in kirromycin production and displays a rarely found three‐domain architecture (AT<jats:sub>1</jats:sub>‐AT<jats:sub>2</jats:sub>‐ER). We demonstrate that the second AT domain, KirCI‐AT<jats:sub>2</jats:sub>, but not KirCI‐AT<jats:sub>1</jats:sub>, is the malonyl‐CoA‐specific AT which utilizes this precursor for loading the acyl carrier proteins (ACPs) of the <jats:italic>trans</jats:italic>‐AT PKS in vitro. In the kirromycin biosynthetic pathway, ACP5 is exclusively loaded with ethylmalonate by the enzyme KirCII and is not recognized as a substrate by KirCI. Interestingly, the excised KirCI‐AT<jats:sub>2</jats:sub> can also transfer malonate to ACP5 and thus has a relaxed ACP‐specificity compared to the entire KirCI protein. The ability of KirCI‐AT<jats:sub>2</jats:sub> to load different ACPs provides opportunities for AT engineering as a potential strategy for polyketide diversification.