Abstract The interaction of an As-rich natural pyrite (FeS2.08As0.043) with aqueous Se(IV) was investigated as a function of pH, ferrous iron concentration, and reaction time. Arsenic is often the most abundant minor constituent of natural pyrite, and is believed to substitute for S in the pyrite structure. EXAFS measurements confirmed the presence of AsS dianion group, with arsenic in the same local configuration as in the arsenopyrite. Speciation studies indicated that Se(0) was the unique reduction product in the pH range 5.05–8.65 over a reaction period of >1month, while trace amounts of FeSeO3 might be formed at pH⩾6.10. At pH>6.07, the formation of Fe(III)-(oxyhydr)oxide is kinetically favored, and it consumed nearly all the aqueous iron, including the extra added Fe2+, thereby inhibiting the formation of the thermodynamically most stable product: FeSe2. After oxidation by Se(IV), the occurrence of surface S0, significant aqueous sulfur deficit, and excessive leaching of arsenic in solution, indicate the preferential release of As impurity via arsenopyrite oxidation. The data suggest that the polysulfide-elemental sulfur pathway, which prevails in acid-soluble metal sulfides, is an important pathway in the oxidation of As-rich pyrite, in addition to the thiosulfate pathway for acid-insoluble pyrite. Control experiments on As-free natural pyrite further support this mechanism. This study confirms the potential of reductive precipitation to attenuate the mobility of Se in the environment and demonstrates that minor elements commonly present in natural pyrite can play a significant role on its dissolution pathway.