In wet soils, oxygen (O2) transport in large structural pores that drain close to saturation limits SOC mineralization and C emissions. However, these effects are still poorly understood because in standard incubation experiments soils are sieved and structural pore networks are destroyed. Our objective was to investigate the effects of soil structure on C mineralization rates under wet soil conditions. We measured CO2 emissions from intact soil cores of contrasting structure taken from conventional tillage vs. no-till treatments in laboratory incubations at pressure heads ranging from saturation to −30 cm. At each drainage step, we used X-ray CT to quantify various metrics of the geometry and topology of air, soil matrix and particulate organic matter (POM). We show that CO2 emissions are regulated by the air-filled porosity connected to the soil surface, as well as by the area of the interface between this connected air phase and the soil matrix and the volume of the matrix located within 2–3 millimetres of the interface and POM in this “active” zone. All four of these variables increase concomitantly with air-entry, although in the case of no-till soils, CO2 emissions increased most rapidly during initial drainage. We attributed this to the more heterogeneous “space-filling” pore structure and a larger fraction of bio-pores found in the no-till cores. These results should help to support the development of improved models of SOC turnover taking into account the effect of soil structure and soil management.