Nature is rich in colors (minerals, plants, microalgae, etc.), and pigment-producing microorganisms (fungi, yeasts, and bacteria) are quite common. Among the molecules produced by microorganisms are carotenoids, melanins, flavins, phenazines, quinones, bacteriochlorophylls, and more specifically monascins, violacein, or indigo. Focus will be first dedicated to Monascus, which is cultivated on solid medium in Asian countries to produce a red colorant named ‘Anka’, used as a food ingredient. Despite the enormous economic potential of Monascus pigment, it does not lead to a commercial exploitation in the Western world, mainly because of ignorance and also reluctance to change from food public agencies. The second and third cases present, respectively, the production of Arpink Red, a molecule with a chromophore of the anthraquinone type, and the biosynthesis of riboflavin, the vitamin B2 but also a yellow food colorant. As most industrial applications in the field of microbial pigments deal with carotenoids, examples were selected such as β-carotene, lycopene, astaxanthin, zeaxanthin, and torulene. Applications are numerous in health supplements, animal feed, nutraceutics, and food colorants. The last part concludes with some prospects for carotenoid production by genetically modified microorganisms, especially directed evolution and combinatorial biosynthesis.