For the last decades, the fate of lignins in soil was analyzed mainly with cupric oxide (CuO) oxidation, which is traditionally used to quantify soil lignin content and characterize its state of degradation. This method presents limitations due to incomplete depolymerization of the lignin structure. In this study, we used a physicochemical soil lignin isolation procedure, which permits recovery of a milled wall enzymatic lignin (MWEL) fraction. Elemental composition and chemical structure of MWEL isolated from plants and soil were characterized. Its incorporation rate into an agricultural loamy soil was studied using stable isotope analyses of MWEL isolated from soils after 0 to 9 years of maize cultivation after wheat. Comparison of MWEL isolated from maize tissues and soil provided information on evolution of the lignin structure once incorporated into soil. We observed aromatic-aliphatic complex formation, which could lead to its sequestration in soil evidenced by increasing MWEL content after 9 years of maize cultivation. The 13C natural abundance of isolated MWEL showed faster incorporation of MWEL (17.4 % of renewed lignins after 9 years) compared to total soil organic matter (9 % of total soil organic carbon (SOC) was renewed). This faster incorporation rate of MWEL compared to bulk soil organic matter is in agreement with lignin turnover observed by CuO oxidation. Radiocarbon dating of MWEL suggested a mean age of around 50 years. We conclude that lignin isolation allows (1) access to a different fraction compared to CuO oxidation and (2) a detailed characterization of lignin transformation in soil. We suggest that interaction with aliphatic compounds could be one possible pathway of lignin preservation in soil.