Pigments can be divided into four categories: natural, nature-identical, synthetic, and inorganic colors. Artificial colorants are the most used in food and pharmaceutical industries because of their advantages related to color range, price, resistance to oxygen degradation, and solubility. However, many natural pigments present health-promoting activities that make them an interesting option for human use and consumption. Natural colorants are derived from sources such as plants, insects, and microorganisms. Carotenoids are natural pigments with important biological activities, such as antioxidant and pro-vitamin A activity, that can be either extracted from plants and algae or synthesized by various microorganisms, including bacteria, yeasts, filamentous fungi, and microalgae. Advantages of microbial production include the ability of microorganisms to use a wide variety of low cost substrates, the better control of cultivation, and the minimized production time. After fermentation, carotenoids are usually recovered by cell disruption, solvent extraction, and concentration. Subsequent purification steps are followed depending on the application. The most prominent industrial applications of carotenoids, considering their health benefits, are in the food, feed, and pharmaceutical industries.