Molecular and compound specific isotope compositions of apolar lipids were characterized in soil mesocosms incubated for 1 year with or without 13C-labelled plant residues and earthworms, in order to investigate, at the molecular scale, the effect of earthworms on the fate of organic matter (OM) in soils. Molecular and isotope composition of long chain alkanes in casts confirmed that earthworms preferentially ingest soil fractions rich in plant debris. Apolar lipid specific isotope composition allowed calculation of the proportion of carbon derived from the labelled residues (Clab). Casts displayed higher Clab values than surrounding soil while soil without earthworm exhibited intermediate Clab. The odd-over-even predominance (OEP) of alkanes suggested they are probably less degraded in casts than in the surrounding soil. Taken together, OEP and Clab values suggested that besides high incorporation of plant residues, earthworms may also favor the preservation of plant apolar lipids in their casts. Additionally, chain length and isotope pattern of alkanes further suggested root lipids were probably less degraded than shoot lipids. High 13C-incorporation level for the bacterial biomarker hopene provided evidence for intense recycling of plant OM and suggested further contribution of bacterial necromass to soil OM.