The continental crust is strongly depleted in iron relative to mid-oceanic ridge basalt, broadly identical to the calc-alkaline magmas, suggesting that calc-alkaline differentiation is key to continent formation. However, it remains contentious as to what drives Fe depletion during magmatic differentiation in the crust. The two competing hypotheses for calc-alkaline differentiation—magnetite versus garnet (± amphibole) fractionation—predict contrasting Fe isotopic fractionation pathways in evolved melts because magnetite preferentially depletes ferric, isotopically heavy Fe whereas garnet (± amphibole) does the opposite. We report whole-rock Fe isotope data for two suites of igneous rocks from the central Andes, which represent magmas traversing normal and thickened arc crust, respectively. The magmas traversing thickened crust show a strong Fe depletion trend and consistently high δ56Fe values (0.14‰ ± 0.02‰, 1 standard deviation [SD]), while those traversing normal crust are less depleted in Fe and show variable δ56Fe values (0.10‰ ± 0.05‰, 1SD). The two Andean suites are both isotopically heavier than Mariana arc (Pacific Ocean) magmas that differentiate along tholeiitic (Fe-enriching) paths. These results confirm that garnet (± amphibole) fractionation/retention is the primary driver of Fe depletion in calc-alkaline magmas, and highlight a role for crustal thickening in generating calc-alkaline magmas.