Zircon grains from the Kiruna iron oxide–apatite (IOA) ore bodies in northern Sweden are distinct in their hafnium and oxygen isotopic ratios compared to zircon grains from adjacent metavolcanic host rocks and related intrusions. Here, we combine these two isotopic systems on previously dated zircon grains to improve our understanding of these ore deposits with a long-debated origin. Contrasting theories for the formation of the Kiruna iron ores suggest either (1) emplacement through immiscible silicate–iron oxide melts or (2) transportation and deposition of iron by hydrothermal fluids. Zircon from the metavolcanic host rocks and intrusions have oxygen isotopic ratios (δ18O ∼3‰) that lie below typical magmatic compositions, which is evidence that roof rocks altered by meteoric water were digested into the magma. In contrast, the ores show an influence of a fluid that is higher in δ18O (∼7‰). Based on these findings, we propose the involvement of episodic magmatic-hydrothermal fluids in the ore genesis of the Kiruna iron ore deposits: (1) the first episode related to a deep-seated magmatism and to regional-scale metasomatic alteration, and (2) a later fluid event related to shallow intrusions and responsible for the ore formation. Distinct differences in the Hf isotopic ratios for host rocks and intrusions (εHfi = −6 to −10, Archean crust) and ore (εHfi = −5 to +3, depleted mantle) further allow us to screen possible fluid sources for their involvement in the ore process.