The autotrophic removal of sulphate and nitrate in bioelectrochemical reactors was investigated at different external voltages (0.2, 0.4, 0.6, 0.8 and 1.0 V) under anaerobic conditions. Sulphate and nitrate removal, nitrite accumulation, reduction trend of nitrate and sulphate and microbial community structure were explored. Results indicate the highest removal efficiencies of nitrate and sulphate at 43.3 +/- 2.8 and 7.1 +/- 0.2 mg.l(-1).d(-1) when the voltage is 0.6 V. Moreover, nitrite accumulation decreases with increased voltage from 0.2 V to 1.0 V. Illumina high-throughput sequencing results show similar richness and diversity of bacterial species with increased voltage from 0.2 V to 0.8 V. However, with further increased voltage to 1.0 V, bacterial diversity and richness decrease significantly. Overall, significant differences in community compositions are observed at different voltages.