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 magmatic13 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 inherits a high Sr/Y and 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.