In this study Shortcut Biological Nitrogen Removal (SBNR), Granular Sequencing Batch Reactor (GSBR), and anaerobic ammonium oxidation (Anammox) were comparatively discussed for combined treatment of anaerobic digester effluent. The experiments were carried out through operating pilot and lab scale reactors. These processes have common ground that biologically removes high strength ammonium and they are cost effective and energy efficient. The SBNR process could remove significant nitrogen from anaerobic digestion effluent without supplementation with additional carbon and alkalinity at a low C/N ratio. The aerobic granular sludge which was generated by the GSBR process demonstrated an effective simultaneous organic and ammonium removal. The Anammox process was successfully started using UASB and SBR. After 100 days, the ammonium removal exponentially increased and finally approached to around 75% in both reactors. However, the high active biomass and the long period, which are needed to start up Anammox process, limited the application of this process.