Plant residues incorporated into soils are subjected to contrasted stabilization and biodegradation processes and may contribute to pools of soil organic matter (SOM) displaying different turnover times. Little is known about the relationship between the chemical structure of plant macromolecules and their long-term turnover in soils. Our research objective was to quantify the in situ turnover of phenols derived from lignin, which is a major component of plant tissues often considered slowly biodegradable relative to total plant organic matter. In this study, we used natural 13C labeling of SOM generated by a 9-year chronosequence of maize C4 crop (δ13C around −12‰) replacing the previous wheat C3 crop (δ13C around −27‰) at the Closeaux experimental field, in France. Here we present the combined applications of CuO oxidation and gas chromatography coupled via a combustion interface to an isotope ratio mass spectrometer (GC/C-IRMS) to follow variations in the isotopic composition of lignin-derived monomers in soils of the wheat–maize transition chronosequence. This study aimed at evaluating: (1) the precision and repeatability of this molecular-level isotopic tracer technique, and (2) its potential for computing the proportion of newly derived C in each lignin phenol. Nine years of maize cropping influenced neither the total organic carbon (OC) content nor the lignin content and biodegradation degree in soil. The total SOM after 9 years of maize cropping was significantly enriched in 13C by 1.4‰ compared to the wheat soil. In the CuO-derived lignin phenols, the variations of 13C contents after 9 years of maize cropping ranged from 4.9‰ to 10.0‰, with an average value for total lignin of 7.3‰. These variations were well above the precision of the analytical method, calculated for maize plant and soils to be in the range 0.2–0.8‰. This study thus demonstrates that the CuO oxidation technique is applicable to the determination of the natural isotopic abundance variations in lignin monomers of soils of a C3/C4 chronosequence. Finally, we could calculate the proportion of newly derived OC after 9 years of maize cropping. This proportion was 9% for total SOM and 47% for lignin, which displayed faster dynamics in this soil than total OC. This study confirms, using in situ labeling technique in combination with lignin monomers analysis after CuO oxidation, that lignin macromolecules are not stabilized as such in these soils.