The necessity to address environmental issues has driven efforts toward exploring sustainable bio-based materials as a viable alternative to conventional energy sources. The current study explores the utilization of cocoa pod husk (CPH) biomass for lignin extraction and cellulose production, aiming to contribute to the eco-friendly production of lignin nanoparticles and bioethanol. A synergistic green deep eutectic solvent (DES) (choline chloride/citric acid)-microwave method was employed to effectively fractionate CPH biomass, resulting in an impressive 77.58% lignin removal at 600 W microwave power. The extracted lignin (211.56 mg/g biomass) was utilized to synthesize lignin nanoparticles that were subsequently characterized. Enzyme-driven hydrolysis of the residual cellulose yielded a reducing sugar content of 198.34 mg/g biomass, demonstrating a saccharification efficiency of 70.78%. Fermentation of monomeric sugars by Saccharomyces cerevisiae and Scheffersomyces stipitis, respectively, gave a maximum ethanol yield of 130 mg/g biomass with a high fermentation efficiency (67.17%). The alterations in the CPH's surface structure and morphology following sequential pretreatment were assessed through FT-IR, BET, and SEM analyses, facilitating effective enzymatic hydrolysis. The current investigation adds to the increasing recognition of sustainable approaches in leveraging waste biomass resources toward a more environmentally conscious future.