We identified and quantified specific biomarkers of shoots and roots (cutin and suberin-derived compounds, respectively) of three grassland species (Dactylis glomerata L., Festuca arundinacea Schreb. and Lolium perenne L.) in soil under different land use (grass, crop and bare soil) of the SOERE-ACBB experimental site in Lusignan (France). We also investigated the fate of these markers in soil after conversion from grassland (C3 plants) to Zea mays L. (maize) (C4 plant) with natural 13C isotope abundances. Our results indicated that 9-hydroxy hexadecanedioic acid and 8(9)(10),16-dihydroxy hexadecanoic acid may be used as biomarkers for above-ground biomass, whereas 1,22-docosandioic acid, 22-hydroxy docosanoic acid and 24-hydroxy tetracosanoic acid might be the best below-ground biomarkers for the plants investigated under the experimental conditions studied. The presence, concentration and shoot–root allocation pattern of these markers were different from those described for other species, which demonstrates the importance of verifying biomarker specificity for each species. Concentrations of cutin and suberin were largest in soil under maize and smallest under bare soil; this corresponded to the biomass added to the two soils. Suberin decreased by 40–64% and cutin by 24–40% during a 6-year bare fallow, which indicates that root markers were more sensitive than shoot markers to degradation. Changes in 13C isotopic signatures of specific biomarkers after 6 years of maize showed a faster turnover of root than shoot biomarkers, in spite of the much smaller root inputs from maize than from grasses. The sequestration of suberin in soil was more rapid but less durable than that of cutin.