The mechanism for dioxygen activation represents one of the core issues in metalloenzymes. In most cases, the activation of the O-2 molecule requires additional electrons from an external reducant. However, nonheme hydroxyethylphosphonate dioxygenase (HEPD) and methylphosphonate synthase (MPnS) are exceptional C-H oxygenases. Both enzymes do not utilize reductants, rather they employ directly iron(III)-superoxide species to initiate H-abstraction reactions and lead thereby to catalysis of the C-C cleavage in 2-hydroxyethylphosphonate (2-HEP). Using the recently characterized MPnS structure and QM(B3LYP)/MM-based metadynamics simulations, we deciphered the chemical mechanism for MPnS. Our simulations demonstrate O-2 activation in MPnS is mediated by an adjacent Lysine residue (Lys28) in the active site, leading to an unusual H2O2 intermediate in the reductant-independent nonheme MPnS enzyme. Furthermore, the so-generated H2O, intermediate is subsequently employed in a Fenton-type reaction, leading to a locked center dot OH radical that spontaneously attaches to the substrate carbonyl group. Meanwhile, the proton from the Fe(III) OH is shuttled back to the deprotonated Lys28, affording the Fe(IV)-oxo species that is identified by experiment in HEPD. Thus, our calculations demonstrate an unusual proton-shuttle mechanism for O-2 activation in metalloenzymes.