The Miocene Sarkuh porphyry Cu deposit is located in the southwestern part of Urumieh-Dokhtar Magmatic Arc (UDMA) in Iran. Compared with the neighboring giant Sarcheshmeh porphyry Cu deposit, this is a low-grade sub-economic porphyry Cu system (110 million tons @ 0.26 % Cu) characterized by an unusual abundance of magnetite. The present work tried to answer the question of whether or not there are differences in the hydrothermal system of Sarkuh, resulting in the lack of considerable mineralization. In this way, the mineral associations and EMPA data of magnetite were considered to distinguish the different stages of magnetite crystallization reflecting the magmatic-hydrothermal evolution of the Sarkuh deposit. They include (1) magmatic stage magnetite, including magnetite inclusions within primary silicate minerals (i.e., plagioclase and biotite), (2) pre-ore stage magnetite associated with potassic alteration assemblages, (3) main ore stage magnetite tightly associated with sulfide mineralization, and (4) late stage magnetite forming overgrowths on the sulfides. The results of EPMA analysis confirm that magnetite of these four stages differ in Mn, Fe, Ti, Mg, Al, Cr, and V concentrations. Higher V concentrations are found in the magmatic and pre-ore stages, whereas Al and Si reach the highest in the ore and late stages. Our data show that increasing fluid-rock interaction and changes in the oxygen fugacity, especially during the main ore stage extending to the late stage, are key factors controlling the trace element partitioning of magnetite. Most of ore stage magnetite formed at temperatures >500 °C and high temperatures prevailed during it. Magnetite crystallization after the main stage of sulfide mineralization accompanied by (partial) martitization indicate the increase of oxygen fugacity towards the late hydrothermal stage. This could explain why the ore and late stage magnetites show chemical similarities to those from sulfur-poor iron oxide copper‑gold (IOCG) deposits rather than porphyry deposits.