Lipoyl synthase (LS) catalyzes the final step in lipoyl cofactor biosynthesis, the insertion of two sulfur atoms at C6 and C8 of an (N6-octanoyl)-lysyl residue on a lipoyl carrier protein (LCP). LS is a member of the radical SAM superfamily, enzymes that use a [4Fe-4S] cluster to effect the reductive cleavage of S-adenosyl-L-methionine (SAM) to L-methionine and a 5'-deoxyadenosyl 5'-radical (5'-dA•). In the LS reaction, two equivalents of the 5'-dA• are generated sequentially to abstract hydrogen atoms from C6 and C8 of the appended octanoyl group, initiating sulfur insertion at these positions. The second [4Fe-4S] cluster on LS, termed the auxiliary cluster, is proposed to be the source of the inserted sulfur atoms. Herein, we provide evidence for the formation of a covalent cross-link between LS and an LCP or synthetic peptide substrate in reactions in which insertion of the second sulfur atom is slowed down significantly by deuterium substitution at C8 or by inclusion of limiting concentrations of SAM. The observation that the proteins elute simultaneously by anion-exchange chromatography but are separated by aerobic sodium dodecyl sulfate-polyacrylamide gel-electrophoresis is consistent with their linkage through the auxiliary cluster that is sacrificed during turnover. Mössbauer spectroscopy confirms that one of the two [4Fe-4S] clusters of LS -presumably the auxiliary cluster - is modified or degraded as a function of extent of turnover. Generation of the cross-link species with a small, unlabeled (N6-octanoyl)-lysyl-containing peptide substrate allowed demonstration of both its chemical and kinetic competence, providing strong evidence that it is an intermediate in the LS reaction.