Microbial pigments have great interest within the healthcare industry, as they possess immunosuppressive, antifungal, antiproliferative properties, induce apoptosis, and may have potential for medical applications. The microbes such as Micrococcus, Bacillus, Rhodotorula, Monascus, Phaffia, Sarcina, and Achromobacter have the capability to produce different pigments. Biosynthesis of microbial pigments has been greatly underexplored and a multitude of potentially useful pigments still await discovery. Only less than 1% of the microbial community is estimated to be cultivated in the laboratory and vast diversity of microbial pigments and their encoding biosynthetic gene clusters remain to be exploited. The expansion of eco-friendly technologies in pigment synthesis is of considerable importance to expand their biological applications. Nanotechnology is presently employed as a tool to explore the darkest avenues of medical sciences to combat diseases caused by drug-resistant microbes. This chapter provides the state-of-art knowledge on the synthesis of nanoparticles from pigments and their pharmacological applications. The current limits and future forecasts for the synthesis of pigment-mediated nanoparticles by microorganisms are discussed. Synthesis of pigment mediated nanoparticles and their avenues in pharmacological applications.