Lignin is the second most abundant natural polymer after cellulose, and valorisation of lignin-rich streams has attracted increasing attention recently. This paper presents a novel and sustainable method to recover lignin from Cocoa Bean Shells (CBS) using Deep Eutectic Solvents (DES) and microwaves. A DES containing p-toluenesulfonic acid, choline chloride and glycerol (2:1:1 M ratio) was selected based on its dielectric properties. Under 200 W microwave power, the optimum yield of 95.5 % lignin was achieved at 130 °C and 30 min. DES-extracted lignin exhibited unique structural characteristics including larger particle sizes (242.5 µm D50 size), structural diversity (410.4 µm D90-D10 size) and H/G sub-unit ratio (71.9 %) compared with commercial Kraft lignin (77.2 µm, 157.9 µm and 0.1 % respectively), indicating the potential of DES in the modification and upgrading of lignin for novel value-added products.