The methylerythritol phosphate pathway of isoprenoid biosynthesis is an attractive anti-infective drug target. The last two enzymes of this pathway, IspG and IspH, are [Fe4S4] proteins not produced by humans that catalyze 2H+/2e− reductions with novel mechanisms. In this review, we summarize recent advances in structural, mechanistic and inhibitory studies of these two enzymes. In particular, mechanistic proposals involving bioorganometallic intermediates are presented and compared with other mechanistic possibilities, and inhibitors based on substrate analogs, developed by rational design and compound library screening, are discussed. These results represent the first examples of bioorganometallic catalytic mechanisms of [Fe4S4] enzymes, and open up new routes to inhibitor design targeting [Fe4S4] clusters.