An integrated system for the biological treatment of wastewater and biodegradable organic waste (BOW) was examined. The system consisted of a membrane bioreactor (MBR) for the treatment of sewage and an anaerobic digestion (AD) unit for the treatment of biowaste and sewage sludge. The ‘zero’ waste concept was the driving force for its implementation, targeting at the effective treatment of BOW, sewage sludge and wastewater and at energy and materials recovery. BOW and wastewater were fed to the integrated treatment system to produce treated effluent suitable for irrigation, energy and a stabilized solid to be used as soil improver. The system was operated for one year, from start-up to process optimization. After the start-up, five experimental stages were carried out for the MBR process and four phases for the AD process. Under optimized operating conditions, the MBR achieved 99% removal of ammonium nitrogen, 95% removal of nitrogen and 96% removal of chemical oxygen demand. The treated effluent satisfied the Cypriot water reuse standards. The energy balance showed that the AD required 5% of heat and 3.5% of electricity from the total energy of the produced biogas to maintain its operation. This resulted in 50% of excess heat and 31.5% of excess electricity.