The aim was to investigate how short rotation coppice (SRC) on arable soil in Northern Germany altered the concentrations of soil lipids, and thus, soil organic matter (SOM) quality. The concentrations of organic C and aliphatic lipids were determined in the litter and underlying soil layers under two willow (Salix caprea × viminalis clone 6, S. viminalis clone 78-183) and two poplar (Populus trichocarpa × deltoides cv. Beaupré, P. nigra × maximowiczii cv. Max 4) clones at a 14-year-old SRC and a permanent arable reference site. High organic C concentrations in the topsoil under S. viminalis and P. trichocarpa × deltoides agreed with high concentrations of long C-chain saturated n-alkanoic acids, n-alkanols and n-alkanes. These disproportionally higher concentrations of long C-chain saturated n-alkanoic acids (factor 3.6) and n-alkanols (factor 3.8) under S. viminalis and of n-alkanols (factor 3.9) under P. trichocarpa × deltoides than in an arable reference treatment indicated a lower microbial decomposability and, thus, a clone-specific accumulation of these SOM constituents. The clone-specific enrichments in long C-chain saturated n-alkanoic acids, n-alkanols and n-alkanes indicate that clone selection may be an approach to additional long-term storage of atmosphere CO 2 in the form of stable SOM under SRC.