Natural colouring agents or biopigments, particularly those derived from microorganisms, present an exciting opportunity for extensive research and industrial application. The use of these naturally derived pigments has gained remarkable momentum in the food industry, driven by the increasing consumer preference for safe, functional, and eco-friendly additives. Historical and traditional food practices also reveal a strong foundation for the use of natural colourants in various food products across different cultures. Examples of food items enriched with microbial pigments include wheat rotis, fortified biscuits, white chocolate, meatballs, cookies, and eggs, all of which demonstrate the successful incorporation of these compounds into everyday foods. Yeast-derived bioactive compounds and pigments such as β-carotene, astaxanthin, lycopene and mannoproteins derived from diverse yeast species including Rhodotorula mucilaginosa, Rhodotorula glutinis, Phaffia rhodozyma, Metschnikowia pulcherrimsa, Cryptococcus, Sporobolomyces and Exophiala salmonis offer significant potential for food fortification and functional enhancement. The supplementation of yeast-derived pigments and bioactive compounds into conventional foods not only improves their visual and sensory attributes but also offers substantial health benefits, such as antioxidant, antimicrobial, and immunomodulatory effects. Consequently, the inclusion of these natural pigments can significantly enhance the health-promoting properties and nutritional value of food products, aligning with the global trend toward sustainable and functional foods.