Assessing the organic C (Corg) sequestration in no-till soils under perennial crops requires molecular-level quality indicators. Therefore, we investigated the quality of soil organic matter (SOM) in the topsoil under Salix viminalis L. and Lolium perenne L. at two test sites in Central Sweden. The willow S. viminalis (clone 78021) was grown in short rotation coppice, and the grass L. perenne in an adjacent meadow for 17 (site Ultuna) and 15 years (site Enköping), respectively. The concentrations of aliphatic lipids, determined by gas chromatography/mass spectrometry (GC/MS), as well as the molecular composition and thermal stability of the bulk SOM, determined by pyrolysis-field ionization mass spectrometry (Py-FIMS), were tested as indicators for the crop-specific SOM quality. Larger Corg concentrations (factor 1.4) in the topsoil (site Ultuna) under S. viminalis than under L. perenne corresponded to higher concentrations of summed aliphatic lipids (factor 1.6), mainly saturated n-alkanoic acids (factor 2.1) and n-alkanols (factor 1.5) in the GC/MS-analyses. Moreover, in the willow stand (site Ultuna) at soil depth of 0-10cm disproportionally higher concentrations of saturated n-alkanoic acids (C17-C36) (factor 2.4) and n-alkanes (C21-C36) (factor 2.6) indicated a preferential sequestration of aliphatic C because the bulk Corg concentrations were only larger by factor 1.4. This crop-specific impact on SOM at soil depth of 0-10cm was proven for both test sites. Furthermore, the Py-FIMS showed larger abundances of thermally stabile alkylaromatics (factor 1.4), and non-peptidic N-containing compounds (factor 1.3) in the S. viminalis plot (site Enköping), which supported a crop-specific Corg-sequestration of these compounds. Thus, in summary, accumulations in extracted long C-chain aliphatic lipids and the thermal stability of some substance classes indicated that the Corg sequestration by no-till may be more distinct in soils under S. viminalis than under L. perenne.