The current research project has been devoted to isolating new low cost and eco-friendly phenolic compounds from fruit seeds, peels and vegetables to reduce the atmospheric pollution. Natural phenolic compounds were extracted from different fruit seeds and agriculture waste: P. armeniaca, P. persica, P. domestica and Triticum aesativum. The total phenolic content was quantified, and the maximum value (1 mL extract having 1,933 μg) was found in P. armeniaca seed extract. Phytochemical screening showed that P. armeniaca seeds contain higher amount of alkaloid, tannins, saponins and flavonoid. P. armeniaca seeds enhanced the biotransformation of reactive yellow dye up to 69.89% with maximum laccase (322.45 IU/mL) production. Biodegradation of reactive yellow was only 23.34% without natural redox mediator at sixth day of incubation. Use of P. armeniaca seed stimulators resulted in maximum laccase activity (894.4 IU/mL) with 99.5% rate of removal. UV-Vis, HPLC & FTIR analysis confirmed the transformation of parent dye into various new products. Phytotoxicity study indicated 0% germination index of Avena sativa seeds with reactive yellow, whereas 83% germination index having 100% seed germination while 83% root elongation with treated sample. Thus, the study revealed that the natural phenolic compounds could serve as high potential redox mediators for enhanced laccase-mediated decolorization of reactive yellow dye.