The use of composts in agricultural soils is a widespread practice and the positive effects on soil and plants are known from numerous studies. However, there have been few attempts to compare the effects of different kinds of composts in one single study. The aim of this paper is to investigate to what extent and to which soil depth four major types of composts would affect the soil and its microbiota.In a crop-rotation field experiment, composts produced from (i) urban organic wastes, (ii) green wastes, (iii) manure and (iv) sewage sludge were applied at a rate equivalent to 175kgNha−1yr−1 for 12 years. General (total organic C (Corg), total N (Nt), microbial biomass C (Cmic), and basal respiration), specific (enzyme activities related to C, N and P cycles), biochemical properties and bacterial genetic diversity (based on DGGE analysis of 16S rDNA) were analyzed at different depths (0–10, 10–20 and 20–30cm).Compost treatment increased Corg at all depths from 11gkg−1 for control soil to 16.7gkg−1 for the case of sewage sludge compost. Total N increased with compost treatment at 0–10cm and 10–20cm depths, but not at 20–30cm. Basal respiration and Cmic declined with depth, and the composts resulted in an increase of Cmic and basal respiration. Enzyme activities were different depend on the enzyme and among compost treatments, but in general, the enzyme activities were higher in the upper layers (0–10 and 10–20cm) than in the 20–30cm layer. Diversity of ammonia oxidizers and bacteria was lower in the control than in the compost soils. The type of compost had less influence on the composition of the microbial communities than did soil depth.Some of the properties were sensitive enough to distinguish between different compost, while others were not. This stresses the need of multi-parameter approaches when investigating treatment effects on the soil microbial community. In general, with respect to measures of activity, biomass and community diversity, differences down the soil profile were more pronounced than those due to the compost treatments.