This study focuses on hydrothermal alteration, and more specifically clays, in the geothermal reservoir of Cerro Pabellón in Andean Cordillera, Northern Chile. Although it is the first commercial geothermal power plant in South America with 48 MWe installed and an additional 33 MWe during 2022, the alteration mineralogy of the deep reservoir remains poorly investigated. Cuttings from two deep wells drilled between 500 and 3000 m depth were sampled. The fine-grained clay fraction was analyzed using X-ray diffraction to observe the mineral distribution and variations of crystal structure of the clays. Scanning electron microscopy coupled with energy dispersive spectroscopy allowed us to perform microanalysis of the clays. The results suggest a high heterogeneity of the reservoir in term of alteration: a pervasive alteration dominated by trioctahedral clays was observed in all the samples, whereas a fracture-controlled alteration was only observed locally, dominated by dioctahedral clays. Illite-smectite mixed layers with more than 90% illite typically occur in permeable fracture and fault as a typical clay signature. This study completed an integrated conceptual model of the high enthalpy reservoir (>250 °C). Circulations of a neutral pH Na-K-Cl fluid occur in a wide fracture system connected to highly dipping and NW-striking faults and could extend beyond the Pabelloncito graben.