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Cellulose and lignin, sourced from biomass, hold potential for innovative bioprocesses and biomaterials. However, traditional fractionation and purification methods often rely on harmful chemicals and high temperatures, making these processes both hazardous and costly. This study introduces a sustainable approach for fractionating acacia wood, focusing on both cellulose and lignin extraction using a deep eutectic solvent (DES) composed of choline chloride (ChCl) and levulinic acid (LA). A design of experiment was employed for the optimization of the most relevant fractionation parameters: time and temperature. In the case of the lignin, both parameters were found to be significant variables in the fractionation process (p-values of 0.0128 and 0.0319 for time and temperature, respectively), with a positive influence. Likewise, in the cellulose case, time and temperature also demonstrated a positive effect, with p-values of 0.0103 and 0.028, respectively. An optimization study was finally conducted to determine the maximum fractionation yield of lignin and cellulose. The optimized conditions were found to be 15% (w/v) of the wood sample in 1:3 ChCl:LA under a treatment temperature of 160 °C for 8 h. The developed method was validated through repeatability and intermediate precision studies, which yielded a coefficient of variation lower than 5%. The recovery and reuse of DES were successfully evaluated, revealing remarkable fractionation yields even after five cycles. This work demonstrates the feasibility of selectively extracting lignin and cellulose from woody biomass using a sustainable solvent, thus paving the way for valorization of invasive species biomass.