Soil carbon sequestration (SCS) is a nature-based, low-cost climate mitigation strategy that also contributes to the climate adaptation of agricultural systems. Some land-use and land-management practices potentially lead to an enhancement of the soil organic carbon (SOC) sink, such as no-till, the use of cover crops, leaving residues on fields, improving the variety of legume species in grasslands and reducing grazing intensity. However, uncertainties remain both in estimating and measuring the impact of the application of certain practices, as these vary with the soil, climate and historic land use. IPCC (Intergovernmental Panel on Climate Change) guidelines are commonly used to estimate SOC and SOC sequestration potentials at different tiers. Here, the IPCC’s tier 1 methodology was applied to estimate (1) the sequestration potential of nine mitigation practices and (2) the emission or sequestration potential of four current land-change trends for n = 7092 unique agricultural sites in mainland Portugal. The conversion of irrigated crops to improved grasslands resulted in the highest average unit sequestration (1.05 tC ha⁻¹ yr⁻¹), while cropland conversion to poor degraded pasture (abandonment) resulted in the highest unit SOC loss (−0.08 tC ha⁻¹ yr⁻¹). The abandonment of cropland results in a national SOC loss of up to 0.09 MtC yr⁻¹, while the improvement of poor degraded pastures has the highest national sequestration potential, equal to 0.6 MtC yr⁻¹ (2.2 MtCO_2eq yr⁻¹), about 4% of Portugal’s emissions in 2021, if applied in all managed areas. The results enable a comparison between different practices and land uses; however, to enhance accuracy, a higher tier methodology tailored to the Portuguese context should be developed.