Abstract Iron oxide–Cu–Au (IOCG) deposits encompass a range of ore body shapes, including strata-bound replacement ores and hydrothermal breccias. We use the implicit method to make a detailed three-dimensional geological model of a strata-bound IOCG in the Cloncurry District, the E1 Group, to elucidate structural controls on mineralization. This model is compared with the nearby, world-class, Ernest Henry breccia-hosted IOCG deposit. Cu–Au mineralization in the E1 Group occurs as structurally controlled, mainly strata-bound, replacement bodies hosted in metasedimentary and metavolcaniclastic rocks intercalated with barren meta-andesite. Replacement bodies in the E1 Group conform to a series of NNW-plunging folds formed in regional D 2 during peak metamorphism. Folding was followed by local D 3 /regional D 4 shortening, which formed a dextral, transpressional Riedel brittle to ductile system along the regional Cloncurry Fault Zone. Modelling suggests that much of the Cu–Au mineralization is controlled by synthetic R structures associated with this Riedel system. The deformation sequence at Ernest Henry is comparable, but differences in host rock rheology, permeability and fluid pressure may explain the variation in ore body types and total Cu–Au resource between the two deposits. The results carry implications for other districts containing these styles of IOCG mineralization. Supplementary materials: Sup 1: Probability plots of assay data for modelled elements. Plots made in ioGAS software. Power transform applied to y -axes of all elements. Note that Fe, P and S do not follow normal/log-normal distributions. Sup 2: Summary statistics of assay data for modelled elements. A description of the rock type (lithology) codes used in the geological model are available in Sup 3. The 3D models presented in this paper are available as supplementary data online (Sup 4) and may be viewed in the free Leapfrog Viewer program, which can be downloaded from http://www.leapfrog3d.com/ . These supplementary files are available at https://doi.org/10.6084/m9.figshare.c.3729946