The Molybdenum/Tungsten-bispyranopterin guanine dinucleotides (Mo/W-bisPGD) family of Formate Dehydrogenases (FDHs) plays roles in several metabolic pathways ranging from carbon fixation to energy harvesting owing to their reaction with a wide variety of redox partners. Indeed, this metabolic plasticity results from the diverse structures, cofactor content, and substrates employed by partner subunits interacting with the catalytic hub. Here, we unveiled two non-canonical FDHs in Bacillus subtilis which are organized into two-subunit complexes with unique features, ForCE1 and ForCE2. We show that the ForC catalytic subunit interacts with an unprecedented partner subunit, ForE, and that its amino acid sequence within the active site deviates from the consensus residues typically associated with FDH activity, as a histidine residue is naturally substituted with a glutamine. The ForE essential subunit mediates the utilization of menaquinone as an electron acceptor as shown by the formate:menadione oxidoreductase activity of both enzymes, their copurification with menaquinone, and the distinctive detection of a protein-bound neutral menasemiquinone radical by multifrequency electron paramagnetic resonance (EPR) experiments on the purified enzymes. Moreover, EPR characterization of both FDHs reveals the presence of several [Fe-S] clusters with distinct relaxation properties and a weakly anisotropic Mo(V) EPR signature, consistent with the characteristic Mo/bisPGD cofactor of this enzyme family. Altogether, this work enlarges our knowledge of the FDH family by identifying a non-canonical FDH, which differs in terms of architecture, amino acid conservation around the Mo cofactor, and reactivity.