To increase the knowledge of microbial adaptation for high degradation ability under ammonia stressed conditions, the metabolic performance and the microbial community in a full-scale chicken manure anaerobic digestion (AD) plant, operated over a 10-year, were investigated. The methanogenic pathway employing labeled acetate (2–13C), aceticlastic methanogenesis activity, and the Illumina sequencing of microbiome structure at the plant were analyzed. The obtained results show that this active plant achieved a methane yield of 310 ± 43 mL/g-volatile solids (VS), high stability under an ammonium-N level of 6.2 ± 0.1 g/L, and an organic loading rate of 2.5 g-VS/(L·d). The extremely long adaptation developed the unique microbe communities, and the hydrogentrophic methanogens Methanobrevibacter (76%) and Methanoculleus (18%) were dominant in the main digester. The acetoclastic methanogenic pathway reached 42%, contributing to the deep degradation. The current study thus may lay the foundation for illustrating the successful full-scale AD of nitrogen-rich materials under stressed operating conditions.