Lignin valorization represents a critical challenge in transitioning to sustainable bio-based materials, as current extraction methods often compromise its structural integrity and limit downstream applications. Despite being the most abundant aromatic biopolymer on Earth, lignin’s complex three-dimensional architecture creates significant barriers to its effective utilization. This research introduces a novel approach using strategically designed deep eutectic solvents (DES) to simultaneously extract and modify lignin structure under mild conditions.Our work demonstrates that carefully selected DES compositions can selectively cleave lignin-carbohydrate complexes while preserving key structural features such as β-O-4 linkages, as has been observed by Liu et al. Analysis of lignin extracted using a DES with the biomass retrieved with various added diol components revealed improved molecular weight distribution and structural integrity compared to conventional methods, confirmed by HSQC-NMR. The addition of diols effectively prevented undesired condensation reactions during extraction, addressing a persistent challenge in lignin valorization. We further are exploring hydrophobic-modified DES systems, revealing their capacity to introduce targeted functional groups during extraction, particularly at phenolic hydroxyl positions. This “extraction-modification” approach is ongoing.These findings represent an insight into the field of extracting lignin in deep eutectic solvents and its effect on the lignin structure and feasibility for potential applications.