Magnetite—apatite deposits associated with the Atacama Fault Zone of northern Chile are interpreted here, on field criteria, as being the products either of hydrothermal fluids with a strong magmatic signature, or of late-stage Fe-rich magmas mixed with an aqueous fluid. Even in the Chilean iron belt, apatite-rich magnetite deposits are a rarity. Variations in F- and Cl- contents in apatites, strongly zoned with respect to halogens, are indicative of primary variations in f_HF and f_HCI in the hydrothermal fluids. Small variations in halogen fugacities in the aqueous fluid are capable of buffering large variations in halogen content within apatite crystals in equilibrium with that fluid. The recorded halogen zonation profiles are inconsistent with crystallization of the apatites simply from a volatile-rich, late-stage fractionation Fe-rich magma, or its derived magmatic vapour. It is more likely that they are the result of mineral—fluid buffering with a fluid that represents the mixing of a magmatically-derived aqueous fluid with a meteoric fluid that has variably scavenged Ca and Cl from within the country rocks. The source magma of the former is probably an Fe-P enriched acidic magma, derived by fractionation of primary calc-alkaline basic magmas.