Acid mine drainage (AMD) from historic and abandoned coal mine spoil represents a potential long-term source of contaminants to surface and groundwater. Determining the risk associated within AMD generation and metal(loid) transport from coal mine spoil is complicated by the heterogeneous natural of spoil heaps and mineralogical and hydro(bio)geochemical factors that may limit or promote metal(loid) transport. The current work aims to determine if primary, reduced phases such as pyrite continue to persist in abandoned and historic coal mine spoil. This objective was accomplished through characterization soils undergoing active weathering while developing on coal mine spoil in Appalachian Ohio to determine the factors that might limit oxidative dissolution. Soils in the Huff Run Watershed (Ohio, USA) were sampled at 0–10 cm, 30–40 cm, 70–80 cm, and 110–120 cm depth. X-ray Diffraction (XRD), Scanning Electron Microscopy with Energy Dispersive Spectroscopy (SEM-EDS), and synchrotron-based X-ray Microprobe (XMP) analyses were used to determine the speciation and distribution of metal(loid)s and the minerals they are associated with. The XMP analyses included micro-focused XRD (μ-XRD), X-ray Fluorescence (μ-XRF) element and redox state mapping, and X-ray absorption Near Edge Structure (μ-XANES) Spectroscopy. Soil mineralogy was dominated by quartz, muscovite, kaolinite, and feldspar, with minor amounts of chlorite and other phases including pyrite, arsenopyrite, realgar, orpiment, hematite, and goethite. Soils from all depths contained metal(loid)-sulfide particles with secondary mineral surface coatings, often in physically complex and heterogeneous aggregates that were composed of clay minerals and secondary Fe(III)-(oxy)hydroxides. These assemblages were typically 10–20 μm in diameter, with an individual pyrite particle core grain size ranging from 0.5 to 10 μm, and secondary mineral surface coatings ranging in thickness from undetectable to 1 μm. Within these aggregates, S and As were present as: (1) small (<20 μm) phases that were spatially correlated with Fe and other trace metal(loids) (Cu, Se, and Zn) and identified as metal(loid)-sulfide minerals; and (2) As(III), As(VI), and S(VI) associated with secondary Fe(III)-(oxy)hydroxides. Intermediate S oxidation state was also observed to be associated with remnant coal and organic matter. These results indicate that pyrite and other metal(loid) sulfides are present in soils developing on historic coal mine spoil after several decades since waste emplacement. The persistence of the μm-scale pyrite grains is likely the result of the formation of the secondary mineral surface coatings which can limit complete oxidative dissolution. These phases also play a role in re-sequestration of metal(loid)s release from sulfide mineral weathering. This work highlights the importance for considering AMD generation from non-point sources, and the potential for long-term ecosystem impairment.