In this work, the influence of modified lignin by Deep Eutectic Solvent (DES) as a novel bio coupling agent on the various properties of wood flour- polypropylene composites (WPCs) was investigated. For this purpose, extracted lignin from Bagasse Soda black liquor was modified with Choline chloride–ZnCl2 deep-eutectic solvent (ChCl–ZnCl2 DES) and then different ratios of unmodified and modified lignin (0, 1, 3 and 5 wt%) were added to the wood flour/polypropylene mixture. Different properties of lignin after modification by DES along with physical and mechanical properties of the manufactured composites were measured according to the relevant standard methods. The FTIR analysis indicated that DES- modified lignin has a higher proportion of phenolic hydroxyl groups (1213 cm−1) and a lower one of methoxy groups (2854 cm−1) when compared to virgin lignin. DSC analysis also showed that the glass transition temperature (Tg) of lignin decreased from 90 °C to 80 °C by DES treatment. Based on the results obtained, the physical and mechanical properties of WPCs were continuously improved by increasing the modified lignin content from 1 to 5 wt%. The composites with DES-treated lignin presented lower water absorption and thickness swelling as well as higher flexural, tensile and impact properties compared to those prepared with unmodified lignin at the same fixed level of lignin. Moreover, based on the finding of this research, the composites with 5 wt% DES-treated lignin have relatively better physical and mechanical properties than those made from 2 wt% maleic anhydride polypropylene (MAPP) as a control sample. Modification of lignin with DES improves its uniform dispersion in the polymer matrix according to Scanning Electron Microscopy (SEM) images.