The northern Norrbotten ore province, situated within the Fennoscandian Shield, constitutes a major metallogenic domain in Europe and hosts more than 40 iron oxide-apatite (IOA) deposits, including the Kiirunavaara deposit, the type locality for this deposit type. Although extensive mapping, geochemical, geochronological, and structural studies have refined the conceptual understanding of IOA systems at deposit and district scales, a fully integrated three-dimensional framework that synthesizes this knowledge with regional geological and geophysical datasets has not yet been developed. This study presents an integrated 3D model of the northern Norrbotten ore province that incorporates lithological, structural, and petrophysical constraints with inversions of magnetic and gravity data, as well as available magnetotelluric conductivity models. The geological models delineate the architecture of intrusive suites, supracrustal belts, crustal-scale shear zones, and subordinate brittle–ductile second-order structures, implemented in a voxel-based domain for quantitative spatial integration. Mafic to ultramafic intrusions previously linked locally to IOA genesis are consistently coincident with high-density, magnetically anomalous domains and spatially associated with vertically extensive electrical conductors. These features are interpreted as the upper-crustal expression of a deeper transcrustal conduit system that facilitated magma ascent, fluid migration, and heat transfer. IOA deposits are located within second-order oblique structures intersecting or splaying from first-order structures, and their geometry and extent correlate with diagnostic magnetic signatures characterized by steep gradients, localized highs, and adjacent negative side lobes. These findings refine the metallogenic framework for IOA mineralization in the northern Norrbotten ore province and provide a robust 3D geoscientific basis for testing mineral system hypotheses.