Implementation of ley grassland into crop rotation could have positive influence in soil ecosystem services such as C storage. The periodical changes of land-use plus the in situ labelling given by the introduction of maize crops under ley grassland induce differences in soil organic matter (SOM) that could be traced either by stable isotopes or by the characterization of plant biomarkers such as lignin derived phenols. Evaluation of SOM dynamics is often limited by the complexity of soil matrix. To override these limitations, a hierarchical approach to decompose the soil mosaic into aggregates has been proposed in this study. Soil and plant samples were collected from a long-term experimental area in Lusignan (western France). Soils from four different treatments (bare fallow, permanent maize, permanent grassland, and ley grassland based on 6 years of grassland followed by 3 years of maize) were sampled, fractionated into water stable aggregates, and finally analysed for carbon, nitrogen, and lignin contents, as well as for 13C isotopic signature. Soils under ley and permanent grassland stored higher amount of SOM in larger aggregates and preserved more efficiently the lignin stocks than the corresponding samples under permanent maize. Contemporary, finer fraction of ley grassland showed higher mean residence time of organic carbon, probably due to a legacy effect of the previous years under grassland. Even if maize derived SOM was identified, the grassland footprint was still dominating the ley grassland soils, as described by the principal component analysis. Strong correlation between these results and the quality and stoichiometry of the vegetal litter returned to soil were found, evidencing the needs for a comprehensive evaluation at a molecular level of all the parameters modified by land-use changes, including tillage, to understand the potential for carbon storage of different agroecosystems.