The neutron structure presented here provides a full-atom snapshot of the early catalytic intermediates in the LPMO reaction pathway. Our results provide the first direct observation of a cryotrapped protonated copper-dioxygen species at the LPMO active site. The unique occluded active site environment found in the crystal structure presented here has resulted in stabilization of an activated dioxygen species at the NcLPMO9D active site with joint occupancy as a superoxo intermediate and a hydroperoxo intermediate, potentially to ultimately form H2O2 in the absence of substrate. A second-shell histidine was further observed in a single Ne-protonation state and in the imidazolate form, leading us to postulate that it plays a role in the early stages of dioxygen intermediate protonation in the unique barricaded environment provided by the binding-face to binding-face crystal packing. Although unusual, a neutral histidine functioning as a general acid has been mechanistically proposed for the His95 residue in triose phosphate isomerase and the His98 residue in methylglyoxal synthase. It remains to be determined whether the role of the second shell His157 in protonation of the activated dioxygen species prevails operando when NcLPMO9D is solvent-exposed and intermittently binds substrate. The flexibility of His157 and potentially that of neighboring active site residues may serve a role in catalysis that must be further explored.