It is well known that atmospheric concentrations of carbon dioxide (CO₂) (and other greenhouse gases) have increased markedly as a result of human activity since the industrial revolution. It is perhaps less appreciated that natural and managed soils are an important source and sink for atmospheric CO₂ and that, primarily as a result of the activities of soil microorganisms, there is a soil‐derived respiratory flux of CO₂ to the atmosphere that overshadows by tenfold the annual CO₂ flux from fossil fuel emissions. Therefore small changes in the soil carbon cycle could have large impacts on atmospheric CO₂ concentrations. Here we discuss the role of soil microbes in the global carbon cycle and review the main methods that have been used to identify the microorganisms responsible for the processing of plant photosynthetic carbon inputs to soil. We discuss whether application of these techniques can provide the information required to underpin the management of agro‐ecosystems for carbon sequestration and increased agricultural sustainability. We conclude that, although crucial in enabling the identification of plant‐derived carbon‐utilising microbes, current technologies lack the high‐throughput ability to quantitatively apportion carbon use by phylogentic groups and its use efficiency and destination within the microbial metabolome. It is this information that is required to inform rational manipulation of the plant–soil system to favour organisms or physiologies most important for promoting soil carbon storage in agricultural soil. © 2014 The Authors. Journal of the Science of Food and Agriculture published by JohnWiley & Sons Ltd on behalf of Society of Chemical Industry.