CuO oxidation is traditionally used for soil lignin study, although, like other degradation methods it might give access only to a part of the lignin polymers. For structural characterization, lignins are conventionally isolated from plant material by combining ball-milling, cellulolysis and solvent extraction to recover a milled wall enzymatic lignin (MWEL) fraction. This method might isolate condensed lignins, which are not accounted for CuO oxidation. MWELs are still associated with polysaccharides. This study aimed to evaluate if the MWEL method can be used complementary to CuO oxidation for soil lignin studies. We assessed the purity of isolated lignins by pyrolytic characterization of MWEL as well as the efficiency of the isolation method by characterization of the MWEL-free residues. MWELs isolated from maize stems and leaves and soil were primarily composed of lignin units, with few associated polysaccharides. MWELs isolated from soils were more degraded and contained less polysaccharides than MWEL from maize tissues. Fewer lignin-derived pyrolysis products were detected in the soil residue compared to the residues obtained from plant tissues. The MWEL method appeared very efficient in isolating relatively pure lignins from soil, most probably because the lignin–polysaccharide complex is less intact than in plants.