Microalgae are significant biological resources with numerous biotechnological uses. Microalgae like Spirulina and Chlorella are being mass-produced for health food due to their great nutritional content. A variety of high-value products including polyunsaturated fatty acids (PUFA), pigments such as carotenoids and phycobiliproteins, and bioactive compounds are useful as nutraceuticals and pharmaceuticals, as well as for industrial applications. Microalgae (prokaryotic and eukaryotic) consist of a wide range of autotrophic organisms that grow through photosynthesis just like land-based plants. Their unicellular structure allows them to easily convert solar energy into chemical energy through CO2 fixation and O2 evolution, being well adapted to capture CO2 and store it as biomass. Microalgae and cyanobacteria have an interesting and not yet fully exploited potential in biotechnology. They can be used to enhance the nutritional value of food and animal feed due to their chemical composition, playing a crucial role in aquaculture. Highly valuable molecules like natural dyes (e.g. carotenoids), polyunsaturated fatty acids, polysaccharides, and vitamins of algal origin are being exploited and can be applied in nutritional supplements; cosmetics (e.g. phycocyanin), and, pharmaceuticals. In fact, microalgae and cyanobacteria are able to produce several biologically active compounds with reported antifungal, antibacterial, anticancer, antiviral (e.g. anti-HIV), immunosuppressive, anti-inflammatory, and antioxidant activity. Nowadays, there is a focus on using microalgae in renewable energy sources and environmental applications. The aim of this review is to discuss bioactive metabolites produced by microalgae for possible applications in the biotechnological fields.