Nitrogenases uniquely reduce atmospheric N₂ to bioavailable ammonium. They group into three isoforms that primarily differ in the architecture of their active-site cofactors. A molybdenum or vanadium ion is introduced into a common precursor cluster to form Mo- and V-dependent nitrogenases, respectively. In contrast, the third class of the enzyme only utilizes abundant iron to reduce N₂ under ambient conditions and is consequently of high interest for mechanistic studies and catalyst design. Here we report the three-dimensional structure of Fe-nitrogenase from Azotobacter vinelandii and its FeFe cofactor, a [8Fe:9S:C] cluster with an interstitial carbide and an organic homocitrate ligand at the apical iron that substitutes for Mo or V in the other isoforms. The structure reveals lability of sulfide S2B, the proposed binding site for substrate in other nitrogenases, further supporting a general mechanism of proton and electron transfer for all nitrogenases and all their substrates.