<jats:title>Abstract</jats:title><jats:sec><jats:label/><jats:p>The first genome scale model (GSM) for <jats:italic>Streptomyces leeuwenhoekii</jats:italic> C34 was developed to study the biosynthesis pathways of specialized metabolites and to find metabolic engineering targets for enhancing their production. The model, <jats:italic>i</jats:italic>VR1007, consists of 1,722 reactions, 1,463 metabolites, and 1,007 genes, it includes the biosynthesis pathways of chaxamycins, chaxalactins, desferrioxamines, ectoine, and other specialized metabolites. <jats:italic>i</jats:italic>VR1007 was validated using experimental information of growth on 166 different sources of carbon, nitrogen and phosphorous, showing an 83.7% accuracy. The model was used to predict metabolic engineering targets for enhancing the biosynthesis of chaxamycins and chaxalactins. Gene knockouts, such as <jats:italic>sle03600</jats:italic> (L‐homoserine <jats:italic>O</jats:italic>‐acetyltransferase), and <jats:italic>sle39090</jats:italic> (trehalose‐phosphate synthase), that enhance the production of the specialized metabolites by increasing the pool of precursors were identified. Using the algorithm of flux scanning based on enforced objective flux (FSEOF) implemented in python, 35 and 25 over‐expression targets for increasing the production of chaxamycin A and chaxalactin A, respectively, that were not directly associated with their biosynthesis routes were identified. Nineteen over‐expression targets that were common to the two specialized metabolites studied, like the over‐expression of the acetyl carboxylase complex (<jats:italic>sle47660</jats:italic> (<jats:italic>accA</jats:italic>) and any of the following genes: <jats:italic>sle44630</jats:italic> (<jats:italic>accA_1</jats:italic>) or <jats:italic>sle39830</jats:italic> (<jats:italic>accA_2</jats:italic>) or <jats:italic>sle27560</jats:italic> (<jats:italic>bccA</jats:italic>) or <jats:italic>sle59710</jats:italic>) were identified. The predicted knockouts and over‐expression targets will be used to perform metabolic engineering of <jats:italic>S. leeuwenhoekii</jats:italic> C34 and obtain overproducer strains.</jats:sec>