A two-stage bioreactor was operated for a period of 140 days in order to develop a post-treatment process based on anaerobic bioxidation of sulfite. This process was designed for simultaneously treating the effluent and biogas of a full-scale UASB reactor, containing significant concentrations of NH(4) and H(2)S, respectively. The system comprised of two horizontal-flow bed-packed reactors operated with different oxygen concentrations. Ammonium present in the effluent was transformed into nitrates in the first aerobic stage. The second anaerobic stage combined the treatment of nitrates in the liquor with the hydrogen sulfide present in the UASB-reactor biogas. Nitrates were consumed with a significant production of sulfate, resulting in a nitrate removal rate of 0.43 kgNm(3)day(-1) and ≥92 % efficiency. Such a removal rate is comparable to those achieved by heterotrophic denitrifying systems. Polymeric forms of sulfur were not detected (elementary sulfur); sulfate was the main product of the sulfide-based denitrifying process. S-sulfate was produced at a rate of about 0.35 kgm(3)day(-1). Sulfur inputs as S-H(2)S were estimated at about 0.75 kgm(3)day(-1) and Chemical Oxygen Demand (COD) removal rates did not vary significantly during the process. DGGE profiling and 16S rRNA identified Halothiobacillus-like species as the key microorganism supporting this process; such a strain has not yet been previously associated with such bioengineered systems.