Four 15-L lab-scale continuous stirred tank reactors were operated under mesophilic conditions to investigate the effect of ammonia inhibition. Stable isotope fingerprinting of biogas was applied as a process monitoring tool. Ammonia inhibition was initiated by amendment of chicken manure to maize silage fed reactors. During the accumulation of ammonia, the concentration of volatile fatty acids increased while the biogas production and pH decreased. However, in one reactor, an inhibited steady state with stable gas production even at high ammonia levels was achieved, while the other reactor proceeded to complete process failure. A depletion of the delta(CH4)-C-13 and delta(CO2)-C-13 values preceded the process inhibition. Moreover, the stable isotope composition of biogas also forecasted the complete process failure earlier than other standard parameters. The stable isotope analyses of biogas have a potential for mechanistic insights in anaerobic processes, and may be used to pre-warn process failure under stress conditions. (C) 2014 Elsevier Ltd. All rights reserved.