Modified ADM1_10, a model able to handle microbial diversity in a thermophilic anaerobic digestion of thermal pretreated WAS was used to simulate the behavior of five batch rector configurations with untreated and different thermally pretreated WAS. The objective was to find relationships between thermophilic anaerobic batch reactor performance and Microbial Community Structure (MCS). Results indicated that a variation in WAS pretreatment temperature caused changes on the microbial community structure of the thermophilic reactor. Microbial diversity based on the Simpson’s diversity index was shown to be important in developing a functionally successful anaerobic microbial community. A link between community structure and function, based in Biochemical Methane Potential (BMP) and Volatile fatty acids (VFAs) concentration for Archaea and Bacteria community structure respectively was assessed. Discussion also highlighted that monitoring of digesters might receive a renewed consideration in the next future in order to handle explicitly microbial diversity within the control objectives.