It has become increasingly popular to replace chemically synthesized compounds with natural counterparts mostly found in natural sources, such as natural pigments. The conventional extraction processes for these compounds are limited by the toxicity and flammability of the solvents. To obtain pure extracts, it is always a longer process that requires several steps. Supercritical fluid extraction (SFE) is a cutting-edge green technology that is continuously increasing and expanding its fields of application, with benefits such as no waste produced, shorter extraction time, automation, and lower solvent consumption. The SFE of natural pigments has high potential in food, textiles, cosmetics, and pharmaceuticals; there are a number of other applications that can benefit from the SFE technique of natural pigments. The pigments that are extracted via SFE have a high potential for application and sustainability because of their biological and antimicrobial properties as well as low environmental risk. This review provides an update on the SFE technique, specifically as it pertains to the optimization of health-promoting pigments. This review focuses on antimicrobial pigments and the high efficiency of SFE in extracting pure antimicrobial pigments. In addition, the optimal conditions, biological activities, and possible applications of each category are explained.