The extraction of sustainable colorants requires energy efficient technology for their eco-application in different fields. For current study on nylon fabric, the natural dye from achiote (Bixa orellana) has been extracted in aqueous and acidic media and valorized through microwave (MW) radiation. MW treatment has been applied to both extracted biomolecule and nylon fabric up to 10 min and the dyeing variables were optimized using statistical model. For getting permanent shades eco-salts of Al (III) and Fe (II) as well as biomolecules from waste plant materials (pomegranate and myrobalan) were utilized. ISO methods for assessment of colorfast shades have been employed. It was found that for nylon, by MW treatment of the dye material and polymeric stuff for 4 min, good color yield in terms of color strength (K/S=29.52) is obtained. It has been observed that when MW treated extract (pH=6) is employed at 40 °C for 55 min, good quality shade of high strength is obtained by using selected amounts of eco-chemical and organic molecules. It is concluded that MW treatment should be given to dyeing process for getting effective yield and tannin based green molecules as organic mordant can used to make dyeing process more ecofriendly and sustainable.