Impact of model-based operation of nutrient removing SBRs on the stability of activated sludge population was studied in this contribution. The optimal operation scenario found by the systematic model-based optimisation protocol of Sin et al. (Wat. Sci. Tech., 2004, 50(10), 97-105) was applied to a pilotscale SBR and observed to considerably improve the nutrient removal efficiency in the system. Further, the process dynamics was observed to change under the optimal operation scenario, e.g. the nitrite route prevailed and also filamentous bulking was provoked in the SBR system. At the microbial community level as monitored by DGGE, a transient shift was observed to gradually take place parallel to the shift into the optimal operation scenario. This implies that the model-based optimisation of a nutrient removing SBR causes changes at the, microbial community level: This opens future perspectives to incorporate the valuable information from the molecular monitoring of activated sludge into,the model-based,optimisation methodologies. In this way, it is expected that model-based optimisation approaches will better cover complex and dynamic aspects of activated sludge systems.