When treating effluents from anaerobic processing of organic wastes, the challenge lies in the large quantity of recalcitrant COD and in the high nitrogen content. The data presented in this study illustrate an advanced SBR concept that is able to significantly reduce the organic load. It was found that undigested mashed bio-waste bypassing the anaerobic digestion is highly suitable as an external carbon source to compensate deficiencies of readily biodegradable BOD required for denitrification. In order to utilize the carbon source as efficiently as possible, the SBR was operated in a mode by which nitrification/denitrification is achieved by a shortcut process using nitrite. This procedure reduced the requirement of an external carbon source to only 5% (v/v). Moreover, through an optimized SBR sequence for an influent concentration of 14,000 mg COD/l and 3,800 mg TN/l, nearly complete removal of nitrogen (>95%) was achieved. The average removal rates for COD and BOD were 83% and 86%, respectively. The applied hydraulic retention time (HRT) of the SBR was 6.8 days. The elevated temperature of 30–41°C in the reactor as a result of the high biological activity was advantageous in terms of enhanced reaction kinetics and also provided better process stability.