Windrow composting of source-separated biowaste was studied in a pilot plant in Crete, with regard to abiotic factors, gas concentration in the pile and succession of functional microbial groups. The pH, C/N ratio and VS content, as well as the O(2) and CO(2) concentration, correlated well with composting time, indicating typical composting behaviour. Most of the microbial groups examined exhibited their highest counts towards the end of the thermophilic phase, with declining trends thereafter. The population of total mesophilic and thermophilic bacteria increased during the mild thermophilic phase and followed the temperature decline thereafter. Results on these microbial groups and fungi indicate that the timing of the thermophilic stage in the composting process, in addition to the peak temperature and duration of the stage, affects the microbial succession. Escherichia coli were detected for over 2 months of processing, in spite of the high temperatures achieved; only after about 3 months of composting did its population decline below the detection limit.