Due to its geodynamic location in the Lesser Antilles arc, Basse-Terre of Guadeloupe displays an active volcanism which is favourable to the development of high-enthalpy geothermal energy. An exhumed analogue of the Bouillante geothermal reservoir has been recently characterized in Terre-de-Haut island (Les Saintes archipelago), giving an opportunity to study the cooling of a natural geothermal system and the related alterations. By coupling chlorite geothermometry and primary fluid inclusions in associated zoned quartz crystals located in N70 trending fractures, new insights on the Terre-de-Haut paleo-geothermal evolution can be inferred by distinguishing three new different episodes during functioning and cooling of this system: (i) a temperature of at least 240–270 °C in fluid inclusions trapped in the quartz core, (ii) chlorite formation at about 120 °C, and (iii) temperatures of ~50 °C - or less - in fluid inclusions of the quartz outer growth zones. Fluid inclusions also reveal that the hydrothermal fluid is of low salinity (2 wt% NaCl), probably of meteoric and sea water origin. Additionally, a second type of fluid inclusions observed in a banded quartz vein indicates at least an episode of a CO2-(H2O) fluid, with traces of H2S. Hence, some similarities can be highlighted between Terre-de-Haut and the Bouillante active geothermal systems in term of the highest temperatures of circulation events and gas composition, despite a difference in fluid origin. This study shows that some alteration episodes also occur at low temperature during the cooling of the geothermal system. Moreover, the N70 trending fractures, that have been identified as drains for the hot temperature fluids, have to be considered for future geothermal exploration.