Methanogens were recently shown to reduce pyrite (FeS2) generating aqueous iron-sulfide (FeS(aq)) clusters that are likely assimilated as a source of Fe and S. Here, we compare the phenotype of Methanococcus voltae when grown with FeS2 or ferrous iron (Fe(II)) and sulfide (HS-). Differential proteomic analyses showed similar expression of core methanogenesis enzymes, indicating that Fe and S source does not substantively alter the energy metabolism of cells. However, a homolog of the Fe(II) transporter FeoB and its transcriptional regulator DtxR were up-expressed in FeS2 grown cells, indicating that cells sense Fe(II) limitation. Two homologs of IssA, a protein putatively involved in coordinating thioferrate nanoparticles, were also up-expressed in FeS2 grown cells. We interpret these data to indicate that DtxR cannot sense Fe(II) and therefore cannot down-regulate FeoB. We suggest this is due to the transport of Fe(II) complexed with sulfide (FeS(aq)) leading to excess Fe that is sequestered by IssA as a thioferrate-like species. This model provides a framework for the design of targeted experiments aimed at further characterizing Fe acquisition and homeostasis in M. voltae and other methanogens.