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Protracted magma storage in the deep crust is a key stage in the formation of evolved, hydrous arc magmas that can result in explosive volcanism and the formation of economically valuable magmatic-hydrothermal ore deposits. High magmatic water content in the deep crust results in extensive amphibole ± garnet fractionation and the suppression of plagioclase crystallization as recorded by elevated Sr/Y ratios and high Eu (high Eu/Eu*) in the melt. Here, we use a novel approach to track the petrogenesis of arc magmas using apatite trace element chemistry in volcanic formations from the Cenozoic arc of central Chile. These rocks formed in a magmatic cycle that culminated in high-Sr/Y magmatism and porphyry ore deposit formation in the Miocene. We use Sr/Y, Eu/Eu*, and Mg in apatite to track discrete stages of arc magma evolution. We apply fractional crystallization modeling to show that early-crystallizing apatite can inherit a high-Sr/Y and high-Eu/Eu* melt chemistry signature that is predetermined by amphibole-dominated fractional crystallization in the lower crust. Our modeling shows that crystallization of the in situ host-rock mineral assemblage in the shallow crust causes competition for trace elements in the melt that leads to apatite compositions diverging from bulk-magma chemistry. Understanding this decoupling behavior is important for the use of apatite as an indicator of metallogenic fertility in arcs and for interpretation of provenance in detrital studies. [ABSTRACT FROM AUTHOR]