Many ecosystem services derived from soils depend on their capacity to store organic matter. The aim of this talk is to present results from recent studies concerning biological as well as physico-chemical mechanisms leading to C gain or loss from soils. The importance of stabilisation processes for elevated residence times of bulk soil organic matter (SOM) and specific molecular compounds in different parts of the soil profile will be highlighted. I will present recent advances and changing paradigms concerning the composition and origin of stabilised SOM. Moreover, I will discuss the influence of biological factors, such as microbial diversity and faunal activity on these processes.