Different strategies of anaerobic digestion of chicken manure were compared. Addition of zeolites positively affected the anaerobic digestion process. Stable process was achieved at free ammonia nitrogen level of 0.6–0.8 g L−1. Clostridia, Bacilli and Actinobacteria were the abundant bacteria in all reactors. Methanosarcina and Methanoculleus were the main methanogenic archaea.