This paper comprises a review of the rapidly expanding application of nanoscale mineral characterization methodology to the study of ore deposits. Utilising bismuth sulphosalt minerals from a reaction front in a skarn assemblage as an example, we illustrate how a complex problem in ore petrology, can be approached at scales down to that of single atoms. We demonstrate the interpretive opportunities that can be realised by doing this for other minerals within their petrogenetic contexts. From an area defined as Au-rich within a sulphosalt-sulphide assemblage, and using samples prepared on a Focused Ion Beam-Scanning Electron Microscopy (SEM) platform, we identify mineral species and trace the evolution of their intergrowths down to the atomic scale. Our approach progresses from a petrographic and trace element study of a larger polished block, to high-resolution Transmission Electron Microscopy (TEM) and High Angle Annular Dark Field (HAADF) Scanning-TEM (STEM) studies. Lattice-scale heterogeneity imaged in HAADF STEM mode is expressed by changes in composition of unit cell slabs followed by nanoparticle formation and their growth into "veins". We report a progressive transition from sulphosalt species which host lattice-bound Au (neyite, lillianite homologues; Pb-Bi-sulphosalts), to those that cannot accept Au (aikinite). This transition acts as a crystal structural barrier for Au. Fine particles of native gold track this progression over the scale of several hundred microns, leading to Au enrichment at the reaction front defined by an increase in the Cu gradient (several wt %), and abrupt changes in sulphosalt speciation from Pb-Bi-sulphosalts to aikinite. Atom-scale resolution imaging in HAADF STEM mode allows for the direct visualisation of the three component slabs in the neyite crystal structure, one of the largest and complex sulphosalts of boxwork-type. We show for the first time the presence of aikinite nanoparticles a few nanometres in size, occurring on distinct (111) PbS slabs in the neyite. This directly explains the non-stoichiometry of this phase, particularly with respect to Cu. Such non-stoichiometry is discussed elsewhere as defining distinct mineral species. The interplay between modular crystal structures and trace element behaviour, as discussed here for Au and Cu, has applications for other mineral systems. These include the incorporation and release of critical metals in sulphides, heavy elements (U, Pb, W) in iron oxides, the distribution of rare earth elements (REE), Y, and chalcophile elements (Mo, As) in calcic garnets, and the identification of nanometre-sized particles containing daughter products of radioactive decay in ores, concentrates, and tailings.