Agricultural soils are globally depleted in soil organic carbon (OC) and therefore, they exhibit a high potential for carbon sequestration under appropriate management practices. Several agroecological management practices aim to increase or retain soil OC through increased carbon inputs (e.g. organic amendments and plant litter), alternative cropping systems (e.g. continuous cover crop) and/or measures to reduce soil OC losses (e.g. reduced or no tillage and adaptive grazing). However, the same practices might increase greenhouse gas (GHG) emissions such as CO₂, nitrous oxide (N₂O) and methane (CH₄), restricting their effectiveness to mitigate climate change. To date, we still lack an understanding on the mechanisms and drivers behind increased GHG emissions and their interactions with OC sequestration under different soil and climatic conditions, partly because little is known about how abiotic and biotic factors control the extent to which soils can store OC. Quantifying negative side-effects of increased soil OC sequestration on GHG emissions is necessary to develop appropriate management options that reduce GHGs while increasing soil OC stocks.