Thermophilic anaerobic digestion in compact systems can be an economical and ecological reasonable decentralised process technique, especially for rural areas. Thermophilic process conditions are important for a sufficient removal of pathogens. The high energy demand, however, can make such systems unfavourable in terms of energy costs. This is the case when low concentrated wastewater is treated or the system is operated at low ambient temperatures. In this paper we present experimental results of a compact thermophilic anaerobic system obtained with fluorescent in situ hybridisation (FISH) analysis and mathematical simulation. The system was operated with faecal sludge for a period of 135 days and with a model substrate consisting of forage and cellulose for a period of 60 days. The change in the microbial community due to the two different substrates treated could be well observed by the FISH analysis. The Anaerobic Digestion Model no. 1 (ADM1) was used to evaluate system performance at different temperature conditions. The model was extended to contribute to decreased methanogenic activity at lower temperatures and was used to calculate energy production. A model was developed to calculate the major parts of energy consumed by the digester itself at different temperature conditions. It was demonstrated by the simulation study that a reduction of the process temperature can lead to higher net energy yield. The simulation study additionally showed that the effect of temperature on the energy yield is higher when a substrate is treated with high protein content.