The food specificity of nematodes, their high number of species and high abundance in every habitat where decomposition takes place, indicate that the structure of the nematode assemblage has a high information content. Since nematodes respond quickly to changes in soil management and since the nematode fauna can be efficiently analysed, the structure of the nematode assemblage offers an interesting instrument to assess changes in soil conditions. We studied the effect of five organic amendments on the short-term nematode population dynamics and compared them to minerally fertilised and unfertilised plots. The experiment was started in 2005, and samples were taken in spring and autumn 2006 and spring 2007. In spring 2006, no clear differences among treatments in the diversity of free-living nematodes were observed, probably since the organic amendments were applied only twice, of which the last application was carried out 7 months before the sampling. At the second and third sampling, the enrichment index in the organically amended plots was higher than in the unamended plots, owing to the organic matter application. However, in plots amended with farmyard manure and cattle slurry the number of bacterivores increased significantly, while in the compost plots the fungivorous nematodes tended to be higher. This resulted in a low channel index for the manure and slurry plots, indicating a predominant bacterial decomposition pathway, and a higher channel index in the compost plots, suggesting a greater proportion of fungal decomposition. These assumptions on the decomposition of the applied organic matter were strongly supported by the composition of the soil microbial community, determined through PLFA analysis: in the compost plots the bacteria to fungi ratio was lower than in the manure and slurry plots. At all sampling occasions there was a remarkably lower abundance of plant-parasitic nematodes in plots amended with slurry and manure, indicating a negative impact of both amendments on plant-parasitic nematodes. We can conclude from this study that the fertiliser regimes affected the nematode assemblage, but that more samplings in the future are certainly necessary to assess adequately the impact of the different organic amendments.