The Siah-Kamar porphyry Mo deposit (SKD) is located at the north-western termination of the Urumieh-Dokhtar magmatic arc and it is the only known porphyry Mo ore reserve in Iran. The SKD formed in two main mineralisation stages, at ~33–32 Ma (late-stage, disseminated) and ~ 29–28 Ma (late-stage, high-grade), within a context of a long-lived magmatism. We integrate results from the whole-rock geochemistry, the Osingle bondC stable and Sr isotope systematics across the mineralised alteration zones with the available drilling data (ore element concentration) to define the ore-forming processes leading to Mo enrichment in the SKD. Our investigation shows that CO2 bearing magmatic fluids had the major role in both early and late-stage mineralisation. The Mo shows positive correlation with SiO2 content but a clear negative correlation with W, Cu, and S, due to a delayed precipitation of Mo during the early-stage mineralisation. The released fluids from the new acidic magmas and subsequent fluid-rock interaction in an open-system, primarily assisted by brittle fracturing, and accompanied by cooling and mixing with various amounts of meteoric water and fluid neutralisation, was responsible for the selective ore depletion and Mo-ore enhancement during carbonatisation along structurally-controlled pathways.