Anaerobic digestion of poultry manure poses many challenges due to ammonia inhibition by nitrogen-containing compounds. Here, the effect of NH4Cl or urea-induced inhibition was investigated in bioreactors fed with maize silage or cellulose and compared to previous experiments with chicken manure as ammonia source. The hydrogen and carbon stable isotope compositions of biogas samples were evaluated to assess the shifts in predominant methanogenic pathways during increasing ammonia inhibition. Due to the higher free ammonia concentrations, stronger inhibition was observed in the urea added reactors compared to the NH4Cl treated ones. Collectively, the results suggested that ammonium salts are not really appropriate to investigate ammonia inhibition during anaerobic digestion of manure.