Soil microbial communities live in the soil pore network and therefore the access they have to organic substrate, oxygen and water depends on how this network is structured. In this experimental study, the relationship between soil structure and soil organic matter dynamics was investigated by measuring the kinetics of organic carbon decomposition in samples that varied in the physical structure of the soil pore network. Soil cores with different structures (undisturbed, sieved and disaggregated by agitation in water), but with the same bulk density, were incubated and the mineralisation of native and added (13C-labelled substrates, fructose and vanillin) organic carbon was measured for a period of 127 days. The incubation was commenced after the immediate effects of the perturbations caused by the soil structural treatments had dissipated. At the end of the incubation, the microbial biomass and microbial community structure were determined. It was found that the respiration kinetics were not related to soil structural parameters, which were determined using X-ray micro-CT. The structure treatments had no significant effect on the mineralisation of soil or added organic carbon, despite the significantly different physical environments. However, the microbial community structure of the undisturbed and dispersed samples were significantly different. These results indicate that neither decomposer access to organic substrate nor the environmental conditions in which decomposition occurred were impaired by the soil structure treatments and suggest that the controls on carbon dynamics may take place at scales below those that were manipulated in this experiment.