Geothermal systems in terrains affected by polyphase deformation have reservoirs with a 3D geometry that is always difficult to predict. In this paper we describe a fossil exhumed geothermal system exposed in eastern Elba Island that developed in a polyphase folded and faulted setting, which can help us to understand how geothermal fluids circulate in geological bodies with inherited structures. Geothermal circulation at Elba allowed the deposition of Fe-ore deposits (haematite/magnetite and pyrite) and altered rock volumes, which represent tracers of the palaeo-fluid flow. Normal and oblique-slip faults dissected a polyphase folded metasiliciclastic succession and produced a secondary permeability in the range of 5 × 10−13 to 5 × 10−16 m2. From the permeable fault zones acting as feeder conduits, geothermal fluids permeated the hydraulically connected metasiliciclastic rock bodies previously deformed by two generations of folds. Geothermal fluids followed the already defined geometry, thus giving rise to apparent folded mineralized levels. Fluid migration into the metasiliciclastic rocks was possible due to their chemical aggression, which favoured the dissolution and reprecipitation of quartz, and Fe-oxide and sulphide deposition. Renewed fluids maintained their chemical properties (pH value and temperature, mostly). This conclusion provides inputs for reconstructing geothermal conceptual models and evaluating the geothermal potentiality of exploitable areas developing in similar geological settings.