There is an urgent need to find large-scale efficient solutions for carbon dioxide removal. Organic carbon (sequestration in soils provide low-cost nature-based solutions and a number of management options have been demonstrated to allow for a net uptake of CO2 from the atmosphere, either by increasing biomass inputs to soil (e.g. cover crops, agroforestry, temporary leys) or by decreasing carbon outputs from soil (e.g. by decreasing tillage). As the longevity of soil organic carbon (SOC) sequestration is important for climate change mitigation, arises the question of increasing the persistence of SOC. This may depend on the nature of management options and organic inputs to soil, as we show from a comparison of long-term experiments, but could also be achieved, in theory, by increasing the extent of stabilization processes of soil organic matter, such as physical protection. We explore established facts and paradoxes regarding physical controls on soil organic matter. These are increasingly understood at the scale of the microbial habitat, where reduced accessibility of substrates to decomposers and reduced availability of oxygen limit soil organic matter mineralization in the soil structure. Contrastingly, the effects of reduced soil structure disturbance on soil organic carbon stocks and residence times, via reduced tillage are still elusive.