Soil organic matter (SOM) is a major component of biogeochemical cycles of nutrient elements such as N, P, and S, and its quantity and quality both reflect and control primary productivity. Understanding the fate of SOM may therefore be essential for making land use sustainable. Nevertheless, the mechanisms and rates by which SOM is cycled have eluded researchers. New questions arose because the time-scale of SOM cycling exceeds the life cycle of soil organisms. Progress is achieved by the determination of biomarkers. A biomarker is an organic compound with known origin that can be used as an indicator for the source and transformation of a range of molecules in the environment. We used lignin as molecular markers for plant remains as well as amino sugars and the enantiomers of amino acids as markers for microbial residues and/or cell ageing processes, for instance. We combined these analyses with compound-specific stable isotope determinations for tracing soil organic C and N dynamics in samples from different climates and with different duration of cropping, radiocarbon age and microbial N status. The results indicated that once microorganisms have access to an N source they tend to degrade it completely rather than leaving fragments behind. However, not all N is accessible to microorganisms. Racemization of aspartic acid and lysine provide a clue to an ageing of soil organic C and N, and how it is affected by land use and site properties.