A microbial fuel cell (MFC) was used to study nitrogen dynamics and its feasibility for high strength wastewater treatment. Intermittent aeration was applied on the cathode chamber accomplishing the establishment of a simultaneous nitrifying-denitrifying microbial community. A total of 30.4% of the N-NH4 + migrated through the ion exchange membrane being primarily nitrified at the cathode chamber. When intermittent aeration was applied in the cathode, denitrification also occurred achieving 17.8% of nitrate removal without acetate addition, and 41.2% with acetate addition. The microbial community analysis revealed that the nitrification process at the cathode chamber could be explained due to a high predominance of Nitrosomonas sp. as ammonia-oxidising bacteria and other Comamonadaceae phylotypes as potential denitrifiers. Parallel batch denitrification assays, carried out outside the MFC using the cathode effluent, confirmed the existence of heterotrophic denitrification processes with other well known denitrifying dominant phylotypes enrichment (Burkholderiadaceae, Comamonadaceae, Alcaligenaceae).