The structure of copper sites formed under an oxidative environment and their evolution in the course of the reaction with methane at elevated temperature was investigated by means of Cu K-edge X-ray absorption spectroscopy for a series of copper-containing MFI, MOR, and FAU zeolites. The pretreatment in oxygen at 723 K leads to the formation of copper(II)-oxo sites, whose nature depends on the framework type. Dimeric species are formed in CuMFI material, dimeric and monomeric sites coexist in CuMOR, and agglomerated copper-oxo nanoclusters are found in large-pore copper-containing faujasite (CuFAU). For all studied materials, the reaction with methane resulted in the exclusive formation of copper(I) species; no formation of metallic copper was detected even at 748 K. The nature of formed copper(I) species is governed by the structure of corresponding copper(II) centers. In particular, monomeric and dimeric copper(II)-oxo sites hosted in CuMOR and CuMFI are transformed into isolated copper(I) cations coordinated to ion-exchange positions of the zeolite. Contrarily, copper(II)-oxo clusters present in CuFAU undergo restructuring with only a partial loss of extra-framework oxygen and form aggregated species with a structure similar to that of bulk copper(I) oxide.