Lignin and hydroxycinnamic acids (p-coumaric and ferulic acids), due to their specificity to vascular plants, can be used as indicators of the fate of plant-derived organic matter in soils. Two chemical degradative methods allowing the recovery of total hydroxycinnamic acids and lignin monomers based on alkaline hydrolysis (THA method) and thioacidolysis, respectively, were compared with alkaline oxidation with CuO on soil and maize (Zea mays L.) roots of different genotypes. Thioacidolysis, commonly used in plant science, was applied for the first time to soil in this study and its sensitivity to different levels of organic carbon was assessed. Syringyl, vanillyl, and cinnamic acids (p-coumaric and ferulic acids) as biomarkers of lignin-derived compounds were determined in a long-term soil incubation experiment with added roots of different maize genotypes. The recovery yields of lignin monomers were compared with the CuO oxidation, thioacidolysis, and THA methods. Thioacidolysis was successfully applied to soil amended with maize roots and was shown to better identifying the uncondensed lignin structures in soil, which are more susceptible to biodegradation than condensed structures.