Wastewater from dairy industries, characterized by its high COD content and relative high COD/TKN ratio, requires post-treatment after anaerobic treatment to complete the removal of organic matter and nutrients. Due to its simplicity, robustness and low maintenance costs, sequencing batch reactors (SBR) result in an attractive system, especially in case of small dairy industries in order to comply with the emission standards. The goal of this work was to determine the operational parameters, optimize the performance, and study the stability of the microbial population of a SBR system for the post-treatment of an anaerobic pond effluent. High and stable removal of COD and TKN was achieved in the reactor, which can easily be set up in dairy industries. An active nitrifying population was selected during reactor operation and maintained relatively stable, while the heterotrophic (total and denitrifying) communities were more unstable and susceptible to changes in the operating conditions.