Zircon provides essential information on the age and oxidation state of magmatic systems and can be used to characterize magmatic-hydrothermal Au mineralizing systems. Using the Douay intrusion-related gold system (IRGS) as a type example of Neoarchean syenite-associated mineralization (Abitibi greenstone belt), we demonstrate that zircon from altered quartz-monzonite rocks can also be used to infer the age of a magmatic-hydrothermal event. Here, zircon chemistry is used to identify the following sequence of events at the Douay exploration project: (1) the crystallization of zircon at ~2690 Ma in evolved residual melts with distinct U-contents (quartz-monzonite magma); (2) the extensive radiation damage for the U-rich grains over a period of ~10–15 My; and (3) the alteration of zircon grains at ~2676 Ma by interaction with magmatic-hydrothermal mineralizing fluids derived from syenite and carbonatite intrusive phases. This study also distinguishes extensively altered zircon grains from pristine to least-altered zircon formed in distinct magmatic environments using a Th/U vs. U discrimination diagram.