Ammonia-rich substrates inhibit anaerobic digestion (AD) process and constitute the main reason of low energy recovery in full-scale reactors. It is estimated that many full-scale AD reactors are operating in ammonia induced “inhibited steady-state” with significant losses of the potential biogas production yield. To date there are not any reliable methods to alleviate the ammonia toxicity effect and/or to efficiently digest ammonia-rich waste. In the current study, bioaugmentation as a possible method to alleviate ammonia toxicity effect in a mesophilic continuously stirred-tank reactor (CSTR) operating under “inhibited steady state” was tested. A fast growing hydrogenotrophic methanogen (i.e. Methanoculleus bourgensis MS2T) was bioaugmented in the CSTR reactor at high ammonia levels (5 g NH4+-N L-1). A second CSTR reactor used as control with no bioaugmentation. The results derived from this study clearly demonstrated a 31.3% increase in methane production yield in the CSTR reactor, at steady-state, after bioaugmentation. Additionally, high-throughput 16S rRNA gene sequencing analysis showed a fivefold increase in relative abundance of Methanoculleus spp. after bioaugmentation. On contrary to all methods used today to alleviate ammonia toxicity effect, the tested bioaugmentation process performed without interrupting the continuous operation of the reactor and without replacing the ammonia-rich feedstock.