Copper-exchanged zeolites are a class of redox-active materials that find application in the selective catalytic reduction of exhaust gases of diesel vehicles and, more recently, the selective oxidation of methane to methanol. However, the structure of the active copper-oxo species present in zeolites under oxidative environments is still a subject of debate. Herein, we make a comprehensive study of copper species in copper-exchanged zeolites with MOR, MFI, BEA, and FAU frameworks and for different Si/Al ratios and copper loadings using X-ray absorption spectroscopy. Only obtaining high quality EXAFS data, collected at large k-values and measured under cryogenic conditions, in combination with wavelet transform analysis enables the discrimination between the copper-oxo species having different structures. The zeolite topology strongly affects the copper speciation, ranging from monomeric copper species to copper-oxo clusters, hosted in zeolites of different topologies. In contrast, the variation of the Si/Al ratio or copper loading in mordenite does not lead to significant differences in XAS spectra, suggesting that a change, if any, in the structure of copper species in these materials is not distinguishable by EXAFS.