This study characterizes the effects of fluid migration into a predominantly shale cover which seals the active geothermal system of Mt. Amiata (Tuscany, Italy). During Alpine orogenesis the shale unit was affected by regional metamorphism at the limit of the diagenesis-anchizone. Subsequently, the phyllosilicate clay minerals of the shales underwent significant alteration at diagenetic temperatures (175±25°C as determined by the geochemical model) by the pervasive circulation of fluids activated by the geothermal field. The overall mineralogical assemblages indicate that the main transformations consisted mostly of destabilization of illite and formation of kaolinite together with large amounts of I-S mixed layers, with higher smectite content and decreased Reichweite I-S ordering (from R3 to R1) with respect to the original, unaltered phases. Application of computer modelling indicates that the circulation of CO2-rich geothermal fluids into the shale unit was responsible for the observed phyllosilicate clay mineral transformations.