There is significant interest in improving methanol yields from methane in copper-exchanged zeolites. Interestingly, zeolites with proton, H + , precursors provide greater methanol yields and selectivities than zeolites from sodium, Na + , precursors. There is however no quantitative description of the origins of these differences. Here, we use the density functional theory to probe differences in the properties of copper-oxo species in the 8-membered ring of zeolite mordenite, MOR. We focus only on [Cu 3 O 3 ] 2+ , [Cu 2 O] 2+ , and two [Cu 2 O 2 ] 2+ species in H-MOR and Na-MOR. Our calculations show that these sites are activated at 345−490 °C, with the bis(μ-oxo) dicopper(III) [Cu 2 O 2 ] 2+ moiety being the most stable and [Cu 3 O 3 ] 2+ the least stable. [Cu 3 O 3 ] 2+ and [Cu 2 O] 2+ are capable of activating methane at 200 °C, with similar C−H activation barriers in H-MOR and Na-MOR zeolites. The fate of the methyl group formed from methane C−H activation differentiates the Na-MOR and H-MOR zeolites.Crucially, we show that rebound of the methyl group to an active-site μ-oxo atom favors over-oxidation. Alternatively, the methyl group can be stabilized via exchange with H + /Na + located at remote aluminates. Exchange with Na + does not provide as much stabilization as the μ-(OCH 3 ) intermediate, thus favoring over-oxidation. By contrast, Bro̷ nsted acid sites provide similar levels of stabilization to the μ-(OCH 3 ) intermediate. This is a path to methanol, rather than over-oxidation products. The discrepancy in the stabilizations provided by Na + and H + -aluminate sites is rooted in the electronic structure.