Under autotrophic conditions, we investigated the effects of different current densities on bioelectrochemical denitrification (BED). In this study, nitrate consumption and nitrous oxide (N2O) production, microbial diversity and population dynamics, and denitrification pathway gene expressions were explored in continuous flow BED reactors at different current densities (0.2, 1, 5, 10 and 20 A/m2). We found that, under the autotrophic conditions, N2O accumulation was increased with increase in current density. The maximum rate of denitrification was 1.65 NO3−–N (g/NCCm3.h), and approximately 70% of the reduced N was accumulated as N2O. After each current density was applied, pyrosequencing of the expressed 16S rRNA genes amplified from the cathodic biofilms revealed that that 16 genera were active and in common at all currents, and that eight of those showed a statistically significant correlation with particular current densities. The relative expression of napA and narG was highest, whereas nosZ was low relative to its level in the inoculum suggesting that this could have contributed the high N2O accumulation. Kinetic analysis of nitrate reduction and N2O accumulation followed Michaelis–Menten kinetics. The Vmax for nitrate consumption and N2O accumulation were similar, however the Km values determined as A/m2 were not. This study provides better understanding of the community and kinetics of a current-fed, autotrophic, cathodic biofilm for evaluating its potential for scale-up and for N2O recovery.