Stillage derived from bioethanol production process is a side stream conventionally used as feed additive after a cost intensive dehydration step. From economical and ecological points of view, it also represents an appealing substrate for biogas production. In this work, we examined the biomethanization of thin stillage in a stirred bioreactor under thermophilic conditions (55°C). Different organic loading rates (OLRs) and hydraulic residence times (HRT) were tested over a long period of operation. Using thin stillage as a mono-substrate, the maximum loading rate reached was 2.1 goTS/L/day. However, with the addition of a commercially available iron hydroxide additive, a maximum OLR of 5.9 goTS/L/day was achieved. Gas chromatography-mass spectrometry (GC-MS) and denaturing gradient gel electrophoresis (DGGE) were used to study the metabolites and the microbial population dynamics within the biogas reactor under different process conditions. For all OLRs studied, volatile fatty acids were shown to give a clear indication of reactor instability. Products of aromatic amino acid degradation, especially phenyl acetic acid (PAA), were detected earlier in reactors even at very low OLRs. PAA concentration above 0.25 g/L indicated an unstable reactor performance and values above 0.5 g/L were found to be inhibitory to the biogas production in batch cultures.