A thermophilic pilot scale anaerobic digester treating chicken litter was subjected to pulse loads of ammonia of increasing concentration. A micro gas chromatograph (mu-GC) measured CO2, CH4, N-2, H-2 and H2S in the biogas. In the liquid, NH4-N was measured manually, volatile fatty acids (VFA) were measured manually and with Near Infrared Spectroscopy (NIRS). Within the first 7-24 h after the pulse, the concentrations of isobutyric and iso-valeric acid increased rapidly and were the best indicators of process stress due to ammonia pulses, confirmed by multivariate analysis. NIRS was not capable of accurate prediction of VFA iso-forms most likely due to low concentrations. Propionic acid was persistent. The ammonia pulses caused an overall decrease of biogas production. The biogas composition was not a good indicator of imbalances; little correlation with VFA measurements was observed. (C) 2013 Elsevier Ltd. All rights reserved.