Abstract Fisheries and aquaculture products will have a lead role in satisfying the food requirements of the growing human population. The fish meal required for the manufacture of aquaculture feeds represents a limited resource having high demand. Unconventional sources of nutrients have been intensely researched and among these, the microbial biomass produced from heterotrophic and autotrophic microorganisms has been considered as a promising substitute for animal‐ and plant‐derived ingredients. Several studies have shown that different species of yeast, bacteria and microalgae are viable for high density culture and show excellent nutritional characteristics for terrestrial and aquatic animals. Such features have lead to additional research to upscale production and although production costs are still high; novel, sophisticated methods have focused on utilizing alternative substrates for producing microbial biomass. The aquaculture industry requires renewable nutrient sources that can yield high quality protein and other essential nutrients. In this context, the nutritional characteristics of microorganisms and the emerging technologies aimed to produce microbial biomass allow forecasting increased applications. The present manuscript reviews the current state of the production and use of microorganisms as dietary ingredients in aquaculture nutrition, with emphasis on those showing solid potential as functional additives and fish meal replacement ingredients. A synthesis of recent results on the effects promoted by the dietary inclusion of microbial biomass is presented, underlining the employment of different sources of yeast, bacteria and microalgae and the physiological ability of aquatic animals to utilize these alternative nutrient sources.