The synergetic inhibition of fatty acids accumulation and ammonia on the metabolic capability of methanogens limits the efficiency of nitrogen-rich substrates anaerobic digestion (AD). In this study, AD of chicken manure under different experimental conditions (namely, organic loading rate (OLR) of 1.25, 2.5 and 5 g.TS L−1d−1) with ammonia-stressed system (⁓6000 mg-NH4 +-N/L) were investigated. The results demonstrated an inhibited- steady state of methane production at OLR of 5.0 g.TS L−1d−1 which resulted in up to 30%–37% methane yield reduction. The highest methane yield (356 mL g VSin −1) and organics removal efficiency (66%) were achieved at OLR of 2.5 g.TS L−1d−1 by extending the hydraulic retention time to 40 days. Methanosarcina was found more tolerant to ammonia stress but Methanobacterium and Methanoculleus dominated in the higher methane yield digester. The results indicated that the proper trade-off between high OLR and ammonia inhibition may develop a high efficiency AD for nitrogen-rich materials.