BACKGROUND: Centrate treatment using microalgal-bacterial processes might be limited by the hydraulic retention time (HRT) required to achieve satisfactory chemical oxygen demand (COD) and nutrients removal. Moreover, the poor settling of microalgal biomass still limits the technical and economic performance of microalgal-bacterial processes. In this work, the performance of microalgal-bacterial aggregates (MABAs) supplied with flue gas was investigated as an effective strategy to improve the treatment of centrate from anaerobic digestion of winery wastewater. RESULTS: MABAs supplied with flue gas achieved maximum soluble COD, N-NO 3− , P-PO 4 3− and N-NH 4 + removal efficiencies of 95%, 94%, 100%, and 100%, respectively, in five-fold centrate dilution within 7 days of operation. Centrate turbidity or its components did not hinder the performance of the MABAs under the conditions tested and no aggregates were formed in controls without MABAs inoculation. The mean diameter of the MABAs after centrate treatment was the same or even larger than that of the aggregates of the inoculum. Scanning electron microscopy analyses showed that the liquid medium composition influenced the structure and the type of microalgae cells established in the MABAs. CONCLUSION: MABAs-based centrate treatment supported by flue gas is a promising technology for improving COD and nutrients removal from centrate as well as further biomass harvesting.