Microcystis spp., are Gram-negative, oxygenic, photosynthetic prokaryotes which use solar energy to convert carbon dioxide (CO2) and minerals into organic compounds and biomass. Eutrophication, rising CO2 concentrations and global warming are increasing Microcystis blooms globally. Due to its high availability and protein content, Microcystis biomass has been suggested as a protein source for animal feeds. This would reduce dependency on soybean and other agricultural crops and could make use of “waste” biomass when Microcystis scums and blooms are harvested. Besides proteins, Microcystis contain further nutrients including lipids, carbohydrates, vitamins and minerals. However, Microcystis produce cyanobacterial toxins, including microcystins (MCs) and other bioactive metabolites, which present health hazards. In this review, challenges of using Microcystis blooms in feeds are identified. First, nutritional and toxicological (nutri-toxicogical) data, including toxicity of Microcystis to mollusks, crustaceans, fish, amphibians, mammals and birds, is reviewed. Inclusion of Microcystis in diets caused greater mortality, lesser growth, cachexia, histopathological changes and oxidative stress in liver, kidney, gill, intestine and spleen of several fish species. Estimated daily intake (EDI) of MCs in muscle of fish fed Microcystis might exceed the provisional tolerable daily intake (TDI) for humans, 0.04 μg/kg body mass (bm)/day, as established by the World Health Organization (WHO), and is thus not safe. Muscle of fish fed M. aeruginosa is of low nutritional value and exhibits poor palatability/taste. Microcystis also causes hepatotoxicity, reproductive toxicity, cardiotoxicity, neurotoxicity and immunotoxicity to mollusks, crustaceans, amphibians, mammals and birds. Microbial pathogens can also occur in blooms of Microcystis. Thus, cyanotoxins/xenobiotics/pathogens in Microcystis biomass should be removed/degraded/inactivated sufficiently to assure safety for use of the biomass as a primary/main/supplemental ingredient in animal feed. As an ameliorative measure, antidotes/detoxicants can be used to avoid/reduce the toxic effects. Before using Microcystis in feed ingredients/supplements, further screening for health protection and cost control is required.