Résumé : Understanding metals circulation-mineral deposits formation in mafic-hosted volcanogenic massive sulfide (VMS) deposits is important to increase knowledge of seafloor hydrothermal alteration processes and ocean-crust evolution. This study aims to combine Cu, Zn and Fe non-traditional stable isotopes with major and trace elements, as well as with petrographic features of the various parts in the Troodos VMS. It is the first time that the complex behavior of non-traditional stable isotopes will be investigated during different alteration processes (from high- to low-temperature) within a hydrothermal system and fingerprint the primary versus the secondary mineralization zones. The mines of Agrokipia, Kambia, Troulli, Skouriotissa (Phoukassa, Three Hills and Phoenix open pits), West Apliki, North and South Mathiatis were sampled for (i) host-rock alteration, (ii) primary versus secondary ore enrichment zone alterations and (iii) weathering supergene alteration observed in the leached caps of the hydrothermal system. Altered pillow lavas, hosting the VMS ore deposits, display basaltic-picritic to basaltic-andesitic geochemical compositions, characterized by low-temperature hydrothermal alteration (<250°C). Based on geochemical affinities (e.g., REE), they have been divided into four different groups, where Groups 1 and 3 indicate a depleted MORB-source, Group 2 illustrates a boninitic source, and Group 4 a more alkaline origin. During alteration, significant enrichment in K, Cu and Zn were displayed, in contrast to REE immobility due to acidic pH conditions and available ligands, which do not facilitate their mobilization. The Groups 1 and 3 of altered pillow lavas, indicating variably depleted MORB-type sources, show the largest Cu isotopes variation (both negative and positive δ65Cu values) compared to Groups 2 and 4, presenting a consistent isotopic behavior towards heavy Cu and Zn isotope compositions. The differences in Cu and Zn isotope fractionation in the Troodos pillow lavas between the groups reflect their sources and the different depletion degree of the latter, demonstrating that the Earth’s lithospheric mantle is heterogenous regarding δ65Cu and δ66Zn. In addition, it is linked to low-temperature effect during alteration, which favored heavy Cu and Zn isotope compositions in Groups 2 and 4, in contrast to Groups 1 and 3. The high-temperature hypogene mineralization zone is represented by pyrite and chalcopyrite, while samples, consisting of secondary Cu-rich mineral phases (e.g., chrysocolla, azurite) represent the low-temperature supergene enrichment zone. A general depletion in heavy 65Cu occurred due to mixing of seawater with the hydrothermal fluid, which suggests that 63Cu was favored to be removed from the latter and introduced in the sulfides during the formation of the primary pyrite and chalcopyrite, while the heavier 65Cu remained in the primary high-temperature hydrothermal fluid. Further depletion in heavy Cu isotopes was displayed due to the continuous oxidation of the primary mineral into a secondary Cu-enriched zone. All the examined sulfides from the Skouriotissa VMS mine, except the supergene ore samples, show negative δ66Zn values due to seawater-hydrothermal fluid mixing. However, the lack of significant Zn isotopes fractionation in the secondary enrichment zone may be attributed to the nature of such mineral phases, which are not rich in Zn concentration. However, physicochemical parameters like temperature and pH changes cannot be totally excluded. In addition, gossans and umbers were identified covering the Cyprus-type VMS systems, implying low-temperature weathering alteration and derivation from high-temperature hydrothermal fluid in a black smoker environment, respectively. It is highlighted that extreme weathering alteration causes large Cu, Zn and Fe isotope fractionation compared to high-temperature alteration environments with a general trend towards lighter isotopic compositions. Low-temperature conditions during weathering processes has a clear impact on non-traditional stable isotopes fractionation. The narrower Cu, Zn and Fe isotope compositions range, which is observed in the umber samples is attributed to the adsorption process. During the latter, Fe- and Mn-rich phases absorb such metals under a wide range of temperature and pH conditions, resulting in limited isotopes fractionation. For example, Zn fractionation usually does not exceed the 0.5‰. It is suggested that integrated Cu, Zn and Fe isotopic analysis provides a powerful geochemical tool to fingerprint all the alteration zones of the Cyprus-type VMS hydrothermal systems from high- to low-temperature conditions. Hence, this is combined with various physicochemical conditions (e.g., temperature and pH), while other parameters like redox chemical reactions, seawater-hydrothermal fluid mixing and adsorption process could significantly favor or not Cu, Zn and Fe isotopes fractionation.