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Agriculture is being called upon to increase carbon (C) storage in soils to reduce greenhouse gas (GHG) accumulation in the atmosphere. Cropping systems research can be used to support GHG mitigation efforts, but we must quantify land management impacts using appropriate assumptions and unambiguous methods. Soil C sequestration is considered temporary because it can be re-emitted as carbon dioxide (CO2) if the effecting practice is not maintained and/or the soil–plant system is disturbed, for example, as the result of changing climate. Because of this, the climate benefit of soil C sequestration depends on the time that C is held out of the atmosphere. When assessing the net GHG impact of management practices, soil C storage is often aggregated with non-CO2 (N2O and CH4) emissions after converting all components to CO2 equivalents (CO2e) and assuming a given time horizon (TH), in what is known as stock change accounting. However, such analyses do not consider potential re-emission of soil C or apply consistent assumptions about time horizons. Here, we demonstrate that tonne-year accounting provides a more conservative estimate of the emissions offsetting potential of soil C storage compared to stock change accounting. Tonne-year accounting can be used to reconcile differences in the context and timeframes of soil C sequestration and non-CO2 GHG emissions. The approach can be applied post hoc to commonly observed cropping systems data to estimate GHG emissions offsets associated with agricultural land management over given THs and with more clearly defined assumptions.