Abstract Carbon (C) sequestration in agricultural soils is forwarded as an option for meeting the objective of making the EU climate neutral by 2050, but the efficiency is questioned due to the non-permanent nature of soil organic carbon (SOC) stocks. The purpose of this study is to examine cost-effective strategies for enhancing C sequestration in agricultural soil across 26 EU countries from 2020 to 2050 while accounting for non-permanence. We develop a dynamic and spatially disaggregated cost-effectiveness model considering three measures: reductions in grain and straw harvests and catch crop cultivation, used to compare the minimum costs of meeting annual national and EU level targets for either sequestration or emissions. The results show that national targets are about 2.6 times more costly than the corresponding EU targets, and emission targets are about 2.5 times more expensive than the corresponding sequestration targets. Findings suggest C sequestration in agricultural soils has the potential to mitigate approximately 38 million tonnes of carbon dioxide equivalents (CO 2 e) annually from 2020 to 2050 at a marginal cost of approximately 64 euro per tonne. If emissions are targeted, the same mitigation could be achieved at a marginal cost of about 183 euro per tonne. The use of annual targets implies the shadow price on C sequestration in soils is jointly determined by the target stringency in preceding, contemporary, and future time periods. The highest shadow price is found around the year 2030. This suggests the use of temporally varying economic incentives for C sequestration in agricultural soils.