Nitrogen is essential for microbial growth during anaerobic digestion. However, high-nitrogen substrates exceeding inhibition level for microorganisms entering the anaerobic digestion system can disrupt nutrient balance, inhibit microbial growth, and reduce biogas production efficiency and yield. This study used two anaerobic digesters with NH3-N levels controlled. Biochar was used to adsorb NH3-N for mitigating inhibition for methanogens. Results provided a strategy for applying the control and recovery of NH3-N in a full-scale anaerobic digestion system with high-nitrogen-substrates. Under a feedstock total solid content of 22.7% and a hydraulic retention time of 20 days, the addition of 167 g/L of powdered biochar per feeding could reduce NH3-N by 2.0 g/L. The average adsorption capacity of biochar used in this study was 12.1 mg N/g. The biogas productivity rate in the reactor reached 4.84 L/L-day, and the methane yield was 240.6 L CH4/kg VSfed. The application of biochar effectively improved the adsorption of NH3-N, which mitigated biotoxicity and enhanced the tolerance of microorganisms for higher NH3-N concentrations. The NH3-N in the control group accumulated beyond 8,000 mg/L, which severely inhibited methanogens. As a result, volatile fatty acids accumulated, which caused a pH decrease and ultimately resulted in system failure. The adsorption capacity of Leucaena biochar was relatively low. Thus, alternative biochar with higher adsorption capacities or appropriate modification techniques should be considered to enhance NH3-N adsorption before adding it to the digester.