Numerous studies have shown the relationship between alteration mineralogy and the characteristics of a geothermal system, as well as the fluid–rock interaction processes. Secondary minerals in such systems have been described as dependent on temperature, pH, fluid composition and lithology, with these being the main factors controlling their formation and characteristics. In this new study we establish a detailed hydrothermal mineralogy and depth zoning associated to the geothermal system of the Irruputuncu volcano. This is a currently active volcano with geothermal manifestations and is mainly composed of andesitic to dacitic lavas built on top of various ignimbrites and older lava flows. Samples were obtained from two continuous drill cores from wells PGC-01 and PGC-02. Petrographic analysis and X-ray diffraction data have shown the presence of calcite and anhydrite in association with clay minerals and interstratified clays as the main secondary mineralogy. Characterization of alteration mineralogy allowed to identify boiling and mixing of fluids as the main hydrothermal processes involved in their formation. It also permitted the identification of two alteration types, an argillic/intermediate argillic and a subpropylitic, reflecting temperatures near the 100–200 °C range and neutral to slightly acidic fluids. Secondary minerals distribution and alteration style were also used to distinguish different zones within the system, which were mainly associated with variations in permeability and fluid chemistry. Lastly, a model was developed clearly explaining previous interpretations of mineralogy and apparent electrical resistivity, giving a framework for future geothermal development in Chile and evidencing that factors such as fluid chemistry, lithology and permeability can play an equal or higher role than temperature in similar systems.