A novel integrated bio-electrochemical system with sulfur autotrophic denitrification (SAD) and electrocoagulation (BESAD-EC) system was established to remove nitrate (NO3−-N) and phosphorus from contaminated groundwater. The impacts of a current intensity gradient on the system’s performance and microbial community were investigated. The results showed that NO3−-N and total phosphorus (TP) could be effectively removed with maximum NO3−-N reduction and TP removal efficiencies of 94.2% and 75.8% at current intensities of 200 and 400 mA, respectively. Lower current intensities could improve the removal efficiencies of NO3−-N (≤200 mA) and phosphorus (≤400 mA), while higher current intensity (600 mA) caused the inhibition of nutrients removal in the system. MiSeq sequencing analysis revealed that low electrical stimulation improved the diversity and richness of microbial community, while high electrical stimulation reduced their diversity and richness. The relative abundance of some genus involved in denitrification and phosphorus removal processes such as Rhizobium, Hydrogenophaga, Denitratisoma and Gemmobacter, significantly (P < 0.05) reduced under high current conditions. This could be one of the main reasons for the deterioration of denitrification and phosphorus removal performance. The results of this study could be helpful to enhance the nutrient removal performance of bio-electrochemical systems in groundwater treatment processes. Display omitted •Suitable currents could improve the nutrient removal efficiencies.•Higher current intensity (600 mA) inhibited wastewater nutrient removal.•Currents changed the microbial diversity in a bio-electrochemical system.•Some genus involved in nitrate and phosphorus removal reduced under high currents.•Key genus Thiobacillus contributed to better denitrification performances.