This research studies the main challenges to achieve a successful inorganic nitrogen post-treatment of anaerobic effluents in the mainstream. The post-treatment is based on autotrophic nitrogen removal. The challenges are: (i) the short-term effects of organic carbon source, the COD/N ratio and the temperature on the autotrophic nitrogen removal; (ii) the long-term performance of the Anammox process under a low nitrogen sludge loading rate and moderate to low temperatures; (iii) the Anammox cultivation in a closed sponge-bed trickling filter (CSTF) and (iv) the autotrophic nitrogen removal over nitrite in a sponge-bed trickling filter (STF).