Understanding the geochemistry of basalt alteration is central to the study of agriculture systems. Various nano-minerals play an important role in the mobilization of contaminants and their subsequent uptake by plants. We present a new analytical experimental approach in combination with an integrated analytical protocol designed to study basalt alteration processes. Recently, throughout the world, ultra-fine and nano-particles derived from basalt dust wastes (BDW) during “stonemeal” soil fertilizer application have been of great concern for their possible adverse effects on human health and environmental pollution. Samples of BDW utilized were obtained from companies in the Nova Prata mining district in southern Brazil for chemical characterization and nano-mineralogy investigation, using an integrated application of advanced characterization techniques such as X-ray diffraction (XRD), High Resolution-Transmission Electron microscopy (HR-TEM)/Energy Dispersive Spectroscopy (EDS)/(selected-area diffraction pattern) SAED, Field Emission-Scanning Electron Microscopy (FE-SEM/EDS), and granulometric distribution analysis. The investigation has revealed that BDW materials are dominated by SiO2, Al2O3, and Fe2O3, with a complex micromineralogy including alkali feldspar, augite, barite, labradorite, hematite, heulandrite, gypsum, kaolinite, quartz, and smectite. In addition, we have identified a number of trace metals such as Cd, Cu, Cr, and Zn, that are preferentially concentrated into the finer, inhalable, dust fraction and, thus, could present a health hazard in the urban areas around the basalt mining zone. The implication of this observation is that use of these nanometric-sized particulates as soil fertilizer may present different health challenges to those of conventional fertilizers, inviting future work regarding the relative toxicities of these materials. Our investigation on the particle size distribution, nano-particle mineralogy and chemical composition in typical BDW samples highlights the need to develop cleaning procedures to minimize exposure to these natural fertilizing basalt dust wastes and is, thus, of direct relevance to both the industrial sector of basalt mining and to agriculture in the region. Display omitted •Expansion in Brazilian basalt mining studies will increase human health information in this area.•Several samples were advanced nanoparticles techniques.•The compounds showed strong sorption ability to hazardous elements.•The advanced methodology has been applied to investigate elements occurrence and ultra-fine/nano-particles properties.