The Malmberget iron oxide-apatite (IOA) deposit in northern Sweden is one of the largest underground iron ore mine operations in the world with estimated ore reserves in 2015 of 346 million metric tons (Mt) at 42.5% Fe. The underground operation is concentrated in 10 orebodies of 5 to 245 Mt each, which currently produce 17.4 Mt of apatite iron ore per year. Structural investigations were combined with data on hydrothermal mineral assemblages in order to reconstruct the relative timing of ore-forming, deformation, and overprinting hydrothermal events. The results improve the understanding of structural geometries, relationships, and control on orebody transposition in the deposit. A first compressional event (D1) around 1.88 Ga represents the main metamorphic event (M1) in the area and was responsible for a strong transposition of potential primary layering and the orebodies and led to the formation of a composite S0/1 fabric. A subsequent F2 folding event around 1.80 Ga resulted in the formation of an open, slightly asymmetric synform with a steeper southeast limb and a roughly SW-plunging fold axis. The result of structural modeling implies that the ore formed at two separate horizons. The folding was accompanied by stretching, resulting in boudinage of the iron orebodies. D2-related high-strain zones and syntectonic granites triggered the remobilization of amphibole, biotite, magnetite, and hematite and controlled the formation of iron oxide-copper-gold (IOCG)-type hydrothermal alteration, including an extensive K-feldspar alteration accompanied with sulfides, scapolite, and epidote. This shows a distinct time gap of at least 80 m.y. between the formation of iron oxides and sulfides. Brittle structures and the lack of an axial planar parallel fabric in conjunction with previous results suggest upper crustal, low-pressure, and high-temperature conditions during this D2 deformation phase, indicating a hydrothermal event rather than a purely regional metamorphic compression. It is proposed in the present study that the Malmberget IOA deposit was deformed and metamorphosed during a 1.88 Ga crustal shortening event. Moreover, the Malmberget IOA deposit was affected by a 1.8 Ga folding and hydrothermal event that is related to a regional IOCG overprint.