Soil microbial fuel cells (sMFC) are a novel technique that use organic matters in soils as an alternative energy source. External resistance (ER) is a key factor influencing sMFC performance and, furthermore, alters the soil’s biological and chemical reactions. However, little information is available on how the microbial community and soil component changes in sMFC with different ER. Therefore, the effects of anodes of sMFC at different ER (2000 Ω, 1000 Ω, 200 Ω, 80 Ω and 50 Ω) were examined by measuring organic matter (OM) removal efficiency, trace elements in porewater and bacterial community structure in contaminated paddy soil. The results indicated that ER has significant effects on sMFC power production, OM removal efficiency and bacterial beta diversity. Moreover ER influences iron, arsenic and nickel concentration as well in soil porewater. In particular, greater current densities were observed at lower ER (2.4mA, 50Ω) compared to a higher ER (0.3mA, 2000Ω). The removal efficiency of OM increased with decreasing ER whereas it decreased with soil distance away from the anode. Furthermore, principal coordinate analysis (PCoA) revealed that ER may shape the bacterial communities that develop in the anode vicinity but have minimal effect on that of the bulk soil. The current study illustrates that lower ER can be used to selectively enhance the relative abundance of electrogenic bacteria and lead to high OM removal.