Anaerobic microbial technologies can be used for the conversion of organic waste streams to biogas for renewable energy recovery or to carboxylates for bio-chemicals production. The emerging biorefineries generate huge amounts of liquid saline wastewaters that pose certain challenges to these anaerobic microbial processes. Granular microbial entities, which form the basis of the upflow anaerobic sludge blanket technology, are highly susceptible to disintegration due to high salt concentrations. Hence, to enable the necessary treatment of these biorefinery wastewaters, suitable strategies to develop and sustain stable anaerobic granules is essential, which is the main objective of this research project. A novel microscopic method will be optimised and validated for high-throughput granule stability screening. The production of biogas will be targeted by applying different strategies to safeguard the activity of the filamentous Methanosaeta, which act as the “iron in reinforced concrete” in the granule. The transition to fermentation for carboxylate production will be achieved by applying a retroactive approach, using existing biogas producing granules, and a proactive approach, through the application of alternative strategies for carboxylate producing granule stabilisation. The realisation of these objectives will enable the treatment of the, thus far considered, “untreatable” waste streams within the biorefinery and beyond.