In paddy soil the reductive dissolution of iron oxide and the availability of organic matter plays an important role in arsenic release under anaerobic conditions. Microbial fuel cells have been shown to reduce organic matter (OM) content and the rate in which this occurs strongly relate to the external resistance applied. In this study we investigated the effects of bioanode operating at different external resistance on the paddy soil microbial community and iron and arsenic concentration. The results show that MFC can be used to reduce soil pore water iron and arsenic concentration and the extent in which this occurs depend on the external resistance applied. The MFC is able to mitigate arsenic release by decreasing organic matter availability. Furthermore, our finding shows that external resistance had a significant influence on the bacterial community composition that develop on the bioanode however only had minimal effect on the community of the bulk soil. These findings suggest that the sMFC can influence the iron and arsenic concentration by reducing OM content and the microbial community that develop in the bioanode vicinity.