Nutrient-poor grassland on a silty clay loam overlying calcareous debris was exposed to elevated CO2 for six growing seasons. The CO2 exchange and productivity were persistently increased throughout the experiment, suggesting increases in soil C inputs. At the same time, elevated CO2 lead to increased soil moisture due to reduced evapotransporation. Measurements related to soil microflora did not indicate increased soil C fluxes under elevated CO2. Microbial biomass, soil basal respiration, and the metabolic quotient for CO2 (qCO2) were not altered significantly. PLFA analysis indicated no significant shift in the ratio of fungi to bacteria. 0.5 m KCl extractable organic C and N, indicators of changed DOC and DON concentrations, also remained unaltered. Microbial grazer populations (protozoa, bacterivorous and fungivorous nematodes, acari and collembola) and root feeding nematodes were not affected by elevated CO2. However, total nematode numbers averaged slightly lower under elevated CO2 (−16%, ns) and nematode mass was significantly reduced (−43%, P = 0.06). This reduction reflected a reduction in large-diameter nematodes classified as omnivorous and predacious. Elevated CO2 resulted in a shift towards smaller aggregate sizes at both micro- and macro-aggregate scales; this was caused by higher soil moisture under elevated CO2. Reduced aggregate sizes result in reduced pore neck diameters. Locomotion of large-diameter nematodes depends on the presence of large enough pores; the reduction in aggregate sizes under elevated CO2 may therefore account for the decrease in large nematodes. These animals are relatively high up the soil food web; this decline could therefore trigger top-down effects on the soil food web. The CO2 enrichment also affected the nitrogen cycle. The N stocks in living plants and surface litter increased at elevated CO2, but N in soil organic matter and microbes remained unaltered. Nitrogen mineralization increased markedly, but microbial N did not differ between CO2 treatments, indicating that net N immobilization rates were unaltered. In summary, this study did not provide evidence that soils and soil microbial communities are affected by increased soil C inputs under elevated CO2. On the contrary, available data (13C tracer data, minirhizotron observations, root ingrowth cores) suggests that soil C inputs did not increase substantially. However, we provide first evidence that elevated CO2 can reduce soil aggregation at the scale from µm to mm scale, and that this can affect soil microfaunal populations.