Abstract Cu–Mo mineralization and associated hydrothermal alteration zones in the Zefreh porphyry Cu–Mo deposit are a result of the emplacement of the early Miocene granodioritic-to-granitic porphyritic intrusions into the Eocene volcanic rocks (dacites, pyroclastic rocks, and andesitic lavas) during active subduction along the Urumieh–Dokhtar Magmatic Belt (UDMB) of Iran. The compositions of rock-forming minerals, such as plagioclase, amphibole, and biotite, in the granitoids of the Zefreh magmatic suite are used to determine temperature and oxygen fugacity in the magma during crystallization and emplacement. Plagioclase is locally unaltered and ranges widely in composition with reverse, normal, and oscillatory zoning, but there is no evidence of excess aluminum. Primary calcic amphiboles in the granodiorite porphyry are mainly magnesio-hornblende with high Mg#’s. The crystallization temperature of the granodiorite is in the range of 765–867 °C (average 821 ± 28 °C for amphibole–plagioclase geothermometer) and 706–861 °C (average 808 ± 35 °C for amphibole alone). Whereas, the zircon saturation temperature for the Zefreh granodiorite is lower and ranges from 724° to 733 °C (average 729 ± 4 °C). Biotites in the least-altered granodiorite and in the potassic alteration are Mg-rich and Ti-poor, and mainly fall within the fields of phlogopite and re-equilibrated primary biotite, because of their low TiO2 contents (2.7–4.5 wt%, average 3.5 wt%). Copper and molybdenum in the Zefreh porphyry deposit appear to have been transported by Cl-rich hydrothermal fluids as chloride complexes, based on the calculated halogen fugacity ratios of the fluid in equilibrium with hydrothermal biotite that range from 5.0 to 5.4 for log (ƒH2O)/(ƒHF), 4.3 to 4.8 for log (ƒH2O)/(ƒHCl), and –2.0 to –1.4 for log (ƒHF)/(ƒHCl). The calculated fugacity ratios indicate that the biotites equilibrated with hydrothermal fluids that varied in composition, including oxygen, sulfur, and halogen fugacities. The intercept values for biotites from the Zefreh porphyry Cu–Mo deposit [IV(F) = 1.9 to 2.2 and IV(Cl) = –4.8 to –4.3] correspond to those from other well-known porphyry Cu–(Mo–Au) deposits worldwide [IV(F) = 1.5 to 2.8 and IV(Cl) = –5.0 to –3.5]. On the other hand, hydrothermal chlorite and epidote in the propylitically altered granodiorite of the Zefreh deposit are more Fe-rich and Mn-poor than those in some mineralized porphyry systems. The calculated temperatures of chlorite formation by the geothermometer of Cathelineau (1988) are all similar (300–330 °C), suggesting the potassically altered granodiorite was also affected by later, cooler hydrothermal fluids associated with the distal propylitic alteration zone. Disseminated chalcopyrite in the matrix of the potassically and propylitically altered granodiorite hosts as much as 1.3 wt% Zn and 0.1 wt% As. Based on whole-rock and mineral compositions, we conclude that the Zefreh magmatic system is similar in many regards to subduction-related ore systems, but it is unlikely to host a major porphyry Cu–Mo deposit.