This study investigates the sequestration and transformation of silver (Ag) and arsenic (As) ions in soil organic matter (OM) at the nanoscale using the combination of atom probe tomography (APT), transmission electron microscopy (TEM), focused ion beam (FIB), ion mill thinning and scanning electron microscopy (SEM). Silver-arsenic contaminated organic-rich soils were collected along the shore of Cobalt Lake, a former mining and milling site of the famous Ag deposits at Cobalt, Ontario, Canada. SEM examinations show that particulate organic matter (OM grains) contains mineral inclusions composed of mainly Fe, S, and Si with minor As and traces of Ag. Four OM grains with detectable concentrations of Ag (by SEM-EDS) were further characterized with either a combination of TEM and APT or TEM alone. These examinations show that As is predominantly sequestered by OM through either co-precipitation with Fe-(hydr)oxide inclusions or adsorption on Fe-(hydr)oxides and their subsequent transformation into scorodite (FeAsO4·2H2O)/amorphous Fe-arsenate (AFA). Silver nanoparticles (NPs) with diameters in the range of ∼5-20 nm occur in the organic matrix as well as on the surface of Fe-rich inclusions (Fe-hydroxides, Fe-arsenates, Fe-sulfides), whereas Ag sulfide NPs were only observed on the surfaces of the Fe-rich inclusions. Rims of Ag-sulfides on Ag NPs (TEM data), accumulation of S atoms within and around Ag NPs (APT data), and the occurrence of dendritic as well as euhedral acanthite NPs with diameters in the range of ∼100-400 nm (TEM data) indicate that the sulfidation of the Ag NPs occurred via a mineral-replacement reaction (rims) or a complete dissolution of the Ag NPs, the subsequent precipitation of acanthite NPs and their aggregation (dendrites) and Ostwald ripening (euhedral crystals). These results show the importance of OM and, specifically the mineral inclusions in the sequestration of Ag and As to less bioavailable forms such as acanthite and scorodite, respectively.