The aim of this paper was to synthesize a series of investigations from a long-term field experiment addressing the turnover of organic matter in soil. This paper is based on four organic matter inputs (soil treatments): none (fallow), small amounts of roots+stubble cropped without N fertilizer (no-N), moderate additions of animal manure, and moderate additions of peat. After 42 years, soil carbon stocks declined in the fallow and no-N treated soil but increased in the animal manure and peat-amended soil. Gentle fractionation of soil particles and aggregates revealed that the silt-sized fraction contained most of the soil C and was most responsive to changes in input of organic matter. The clay-sized fraction ( clay > fine sand > coarse sand. The highest natural abundance of 13C and 15N was found in the clay-sized fraction, the fallow being most enriched in 13C and the animal manure-treated soil in 15N, indicating that the organic matter of the clay-sized fraction had been turned over most intensively. The 13C inventory showed that the transfer from silt- to clay-sized carbon was most intensive in the soil treated with animal manure and least intensive in the peat-treated soil. Bacterial diversity increased from sand- to clay-sized fractions revealed by 16S rRNA genes. Fungal activity was highest in coarse-sized fractions as indicated by enzyme measurements. The quality and amount of organic matter input had no significant effect on the community structure of soil bacteria.