Agricultural production systems have to combine management practices in order to sustain soil quality and also pro®tability. We investigated microbial biomass and size-density fractions of soils from a long-term field trial set up in 1978 at Therwil, Switzerland. It compares the economic and ecological performance of organic and conventional agricultural systems. Main differences of the systems were the amount and form of fertiliser as well as the plant protection strategy, whilst crop rotation and soil tillage were the same. Microbial biomass C and N as well as their ratios to the total and light fraction C and N pools in soils of the organic systems were higher than in conventional systems. This is interpreted as an enhanced decomposition of the easily available light fraction pool of soil organic matter (SOM) with increasing amounts of microbial biomass. The role of microbial biomass as a regulator and light fraction organic matter as an indicator of decomposition is discussed. The presented results indicate that labile pools of SOM are distinctly affected by long-term management practices.