The continuous development of world aquaculture demands new strategies and alternatives aimed to achieve sustainability. The use or microorganisms in aquaculture has greatly evolved during the last two decades. From being considered as a potential threat, during the last years, they have been used as probiotics and inclusively as food source for fish and crustacean. The microbial-based systems represent one of the most viable strategies to achieve a sustainable aquaculture. In short, these systems are based on the promotion of microbial proliferation, either autotrophic or heterotrophic microorganisms; these microbes are expected to use, recycle and transform the excess of nutrients from faeces, dead organisms, unconsumed food and diverse metabolites into biomass, which would be further consumed by the cultured organisms. Successful results on using microbial-based systems have been documented around the world; however, there are key aspects to consider and yet to experiment before a system could be implemented. Some of those aspects are analysed in this manuscript, while new advances in the use of microbial-based systems and recommendations are also presented.