Hydrothermal alteration is a common process in active geothermal systems and can significantly change the physiochemical properties of rocks. To improve reservoir assessment and modeling of high-temperature geothermal resources linked to active volcanic settings, a detailed understanding of the reservoir is needed. The Los Humeros Volcanic Complex, hosting the third largest exploited geothermal field in Mexico, represents a natural laboratory to investigate the impact of hydrothermal processes on the rock properties through andesitic reservoir cores and outcropping analogs. Complementary petrographic and chemical analyses were used to characterize the intensities and facies of hydrothermal alteration. The alteration varies from argillic and propylitic facies characterized by no significant changes of the REE budget indicating an inert behavior to silicic facies and skarn instead showing highly variable REE contents. Unaltered outcrop samples predominantly feature low matrix permeabilities (< 10–17 m2) as well as low to intermediate matrix porosities (< 5–15%), thermal conductivities (0.89–1.49 W m−1 K−1), thermal diffusivities (~ 0.83 10–6 m2 s−1), and sonic wave velocities (VP: ~ 2800–4100 m s−1, VS: ~ 1600–2400 m s−1). Average magnetic susceptibility and specific heat capacity range between 2.4–7.0 10–3 SI and 752–772 J kg−1 K−1, respectively. In contrast, the hydrothermally altered reservoir samples show enhanced porosities (~ 7–23%), permeabilities (10–17–10–14 m2), and thermal properties (> 1.67 W m−1 K−1; > 0.91 10–6 m2 s−1), but a significant loss of magnetic susceptibility (10–3–10–6 SI). In particular, this latter characteristic appears to be a suitable indicator during geophysical survey for the identification of hydrothermalized domains and possible pathways for fluids. The lack of clear trends between alteration facies, alteration intensity, and chemical indices in the studied samples is interpreted as the response to multiple and/or repeated hydrothermal events. Finally, the proposed integrated field-based approach shows the capability to unravel the complexity of geothermal reservoir rocks in active volcanic settings.