SUMMARY Within the iron metallogenic province of southeast Missouri, USA, there are several mines that contain not only economic iron resources, magnetite and/or hematite, but also contain rare earth elements, copper and gold. An area including three major deposits, Pea Ridge, Bourbon and Kratz Spring, was selected for detailed modelling for the upper crustal magnetic susceptibility and density structures. For the study area, ground gravity and high-resolution airborne magnetic and gravity gradiometry data sets are available. An efficient and novel joint inversion algorithm for the simultaneous inversion of these multiple data sets is presented. The Gramian coupling constraint is used to correlate the reconstructed density and magnetic susceptibility models. The implementation relies on the structures of the sensitivity matrices and an efficient minimization algorithm to achieve significant reductions in the memory requirements and computational costs. Consequently, it is feasible to use a laptop computer for the inversion of multiple data sets, each containing thousands of data points, for the recovery of models on the study area, each including approximately one million model parameters. This is the first time that these multiple data sets have been simultaneously inverted for this area. The L1-norm stabilizer is used to provide compact and focused images of the ore deposits. For contrast, independent inversions of each data set are also discussed. In general, our results provide new insights about the concealed ore deposits in the Mesoproterozoic basement rocks of southeast Missouri. Both short- and long-wavelength anomalies exist in the recovered models; these provide a high-resolution image of the subsurface. The geometry and physical properties of the known deposits are determined very well. Additionally, some unknown concealed deposits are revealed; these could be economically valuable and should be considered in future geophysical and geological investigations.