The stoichiometric conversion of methane to methanol by Cu-exchanged zeolites can be brought to highest yields by the presence of extraframework Al and high CH4 chemical potentials. Combining theory and experiments, the differences in chemical reactivity of monometallic Cu-oxo and bimetallic Cu-Al-oxo nanoclusters stabilized in zeolite mordenite (MOR) are investigated. Cu-L3 edge X-ray absorption near-edge structure (XANES), infrared (IR), and ultraviolet-visible (UV-vis) spectroscopies, in combination with CH4 oxidation activity tests, support the presence of two types of active clusters in MOR and allow quantification of the relative proportions of each type in dependence of the Cu concentration. Ab initio molecular dynamics (MD) calculations and thermodynamic analyses indicate that the superior performance of materials enriched in Cu-Al-oxo clusters is related to the activity of two μ-oxo bridges in the cluster. Replacing H2O with ethanol in the product extraction step led to the formation of ethyl methyl ether, expanding this way the applicability of these materials for the activation and functionalization of CH4. We show that competition between different ion-exchanged metal-oxo structures during the synthesis of Cu-exchanged zeolites determines the formation of active species, and this provides guidelines for the synthesis of highly active materials for CH4 activation and functionalization.