Intensification of animal production led to high amounts of manure to be managed. Biological processes can contribute to a sustainable manure management. This paper presents the biological treatments available for the treatment of animal manure, mainly focusing on swine manure, including aerobic processes (nitrification, denitrification, enhanced biological phosphorus removal) and anaerobic digestion. These processes are discussed in terms of pollution removal, ammonia and greenhouse gas emissions (methane and nitrous oxide) and pathogen removal. Application of emerging processes such as partial nitrification and anaerobic ammonium oxidation (anammox) applied to animal manure is also considered. Finally, perspectives and future challenges for the research concerning biological treatments are highlighted in this paper.