A direct route to convert methane into high-value commodities, such as methanol, with high selectivity is one of the primary challenges in modern chemistry. Copper-exchanged zeolites show remarkable selectivity in the chemical looping process. Although multiple copper species have been proposed as active, an in situ spectroscopic investigation is difficult, because of their similar fingerprints. We used ambient pressure X-ray photoelectron spectroscopy to investigate an actual powder sample. We could discriminate between different types of active species involved in the conversion of methane to methanol over two different copper-exchanged zeolites, namely, mordenite and mazzite. After activation at 400 °C in oxygen, we followed the reaction in situ at 200 °C, switching from methane to water, and followed by a second cycle with anaerobic activation. Our experimental results, combined with theoretical calculations, prove that Cu(II) sites bound to extra-framework oxygen are involved in the reaction, and that their structure, formation, and stabilization depend on the type of zeolite and on the Si/Al ratio. ©