Composting was performed in an 800-L box and a 500-L, reactor system. The material used was shredded straw of Miscanthus with pig slurry added as a nitrogen source. Chemical and microbial parameters were measured at five degree temperature intervals until the end of the heating phase and then with increasing intervals during the remaining experiment. In both systems, major losses of carbon occurred during and after the thermophilic phase as a result of degradation of hemicellulose, followed by degradation of cellulose. Total amounts of phospholipid fatty acid (totPLFA) and adenosine triphosphate (ATP) were used as indirect estimates of microbial biomass. These methods correlated well over time, when the limitations of the method for the determination of ATP were taken into account. Microbial biomass in the two systems showed similar values when measured by totPLFA. In contrast, microbial biomass measured by ATP content was higher in the box system than in the reactor system. In spite of the differences in chemical and physical properties in the two systems, the distribution of taxonomic groups of microorganisms, indicated by marker PLFAs, showed similar patterns in the two systems, emphasising that in composting systems temperature is the major parameter controlling the composition of the microbial community.