Methyl sulfur compounds are a rich source of environmental sulfur for microorganisms, but their use requires redox systems. The bacterial sfn and msu operons contain two-component flavin-dependent monooxygenases for dimethylsulfone (DMSO2) assimilation: SfnG converts DMSO2 to methanesulfinate (MSI–), and MsuD converts methanesulfonate (MS–) to sulfite. However, the enzymatic oxidation of MSI– to MS– has not been demonstrated, and the function of the last enzyme of the msu operon (MsuC) is unresolved. We employed crystallographic and biochemical studies to identify the function of MsuC from Pseudomonas fluorescens. The crystal structure of MsuC adopts the acyl-CoA dehydrogenase fold with putative binding sites for flavin and MSI–, and functional assays of MsuC in the presence of its oxidoreductase MsuE, FMN, and NADH confirm the enzymatic generation of MS–. These studies reveal that MsuC converts MSI– to MS– in sulfite biosynthesis from DMSO2. •The crystal structure of MsuC from P. fluorescens was solved at 1.69 Å resolution.•MsuC adopts the acyl-CoA dehydrogenase fold and forms a tetramer.•Functional assays confirm MsuC is a two-component flavin-dependent monooxygenase.•Molecular docking identifies a putative methanesulfinate binding site.•Methanesulfinate is enzymatically oxidized in sulfur assimilation from DMSO2.