Emissions of hydrogen sulfide and methane are two of the major concerns in sewers, causing corrosion, odour and health problems. This study proposed a new free ammonia (FA)-based approach for controlling the biological production of sulfide and methane in sewers. This is based on the discovery that the FA contained in urine wastewater is strongly biocidal to anaerobic sewer biofilms. Long-term operation of two laboratory sewer reactors, with one being dosed with urine wastewater and the other being dosed with raw sewage as a control, revealed the effectiveness of the proposed FA approach. The results showed that dosing of real urine wastewater at FA concentration of 154 mg NH3-N/L with exposure for 24 h immediately reduced over 80% sulfide and methane in the experimental sewer reactor, while the time for recovering 50% sulfide and methane production were 6 days and 28 days, respectively. It also showed that intermittent dosing with an interval time of 5-15 days reduced around 60% sulfide on average. As suggested by community analysis, the remaining sulfide might be produced by a sulfate-reducing bacterial genus Desulfobulbus. Collectively, urine is a part of municipal sewage, and thus separation and re-dosing of the urine wastewater into the sewer for sulfide and methane control should enable the minimization of operational costs and environmental impacts, compared with the previous dosing of chemicals.