We have examined a sustainable biorefinery process for the conversion of cotton gin trash (CGT), a waste from the cotton industry to multiple high value products. Herein, we found CGT native lignin to have unique features as it not only contains the p -hydroxyphenyl (H), guaiacol (G) and syringol (S) units, but structures of flavonoids , tyrosine , and phenylalanine associated with it. We have used the lignin-first approach to exploit its features in CGT and depolymerize it using argon gas and ethanol over Pd/C. The results show that 50% of the bio-aromatics is trans -isoeugenol, a precursor to produce vanillin. The cleavage of N-compounds from CGT during the fractionation process follows similar path as the rate of formation of the bio-aromatics. CGT impurities were shown to affect the reusability of the Pd/C catalyst. The fractionated cellulose-rich portion of CGT was converted to 39 mol% (80% purity) of 5-chloromethylfurfural (CMF), and a solid fuel which has a higher heating value of 20 MJ kg −1 . The liquid extract, removed prior to CGT processing, was hydrogenated to produce C 13 –C 17 liquid hydrocarbons , and the solid extract rich in nutrients is suitable for crops and plants growth. • Flavonoid structures and amino acids linked to cotton waste native lignin. • High purity CMF from cotton waste. • Utilizing CGT to generate multiple high value products eliminate wastes. • High yields of trans -isoeugenol, a vanillin precursor from cotton waste. • Chemicals, liquid and solid fuels from cotton waste.