Nitrogen is one of major contaminants in wastewater; however, nitrogen, as bio-elements for crop growth, is the indispensable fertilizer in agriculture. In this study, two-chamber microbial fuel cells (MFCs) were first operated with microorganisms in anode chamber and potassium ferricyanide as catholyte. After being successfully startup, the two-chamber MFCs were re-constructed to three-chamber MFCs which were used to recover the and of synthetic wastewater into value-added nitrogenous fertilizer from cathode chamber and anode chamber, respectively. Ferric nitrate was used as the sole electron acceptor in cathode, which also was used to evaluate the recover efficiency in the case major anion of in cathode. The output voltage of these MFCs was about 600–700 mV at an external load of 500 Ω. About 47% in anode chamber and 83% in cathode chamber could be recovered. Higher current density can selectively improve the recovery efficiency of both and . The study demonstrated a nitrogen recovery process from synthetic wastewater using three-chamber MFCs.