Low carbon strategies recently focus on soil organic carbon (SOC) sequestration potentials from agriculture and forestry, while Life Cycle Assessment (LCA) increasingly becomes the framework of choice to estimate the environmental impacts of these activities. Classic LCA is limited to static carbon neutral approaches, disregarding dynamic SOC flows and their time-dependent GHG contributions. To overcome such limitation, the purpose of this study is to model SOC flows associated with agricultural land use (LU) and the provision of agricultural substrates to transport biofuels, thus generating dynamic inventories and comparatively assessing energy policy scenarios and their climate consequences in the context of dynamic LCA. The proposed framework allows computing SOC from annual and perennial species under specific management practices (e.g. residue removal rates, organic fertiliser use). The results associated with the implementation of three energy policies and two accounting philosophies (C-neutral and C-complete) show that shifting energy pathways towards advanced biofuels reduces overall resource consumption, LU and GHG emissions. The French 2015 Energy Transition for Green Growth Act (LTECV) leads towards higher mitigation targets compared with business-as-usual (BAU) and intermediate (15BIO) policy constraints. C-neutral results show reduced radiative forcing effects by 10% and 34% for 15BIO and LTECV respectively, with respect to BAU. C-complete (i.e. dynamic assessment of all biogenic- and fossil-sourced C flows) results reveal further mitigation potentials across policies, whereof 50%-65% can be attributed to temporal C sequestration in perennial rhizomes. A sensitivity analysis suggests important SOC variations due to temperature increase (+2°C) and changes in residue removal rates. Both parameters affect mitigation and the latter also LU, by a factor of −0.56 to + 5. This article highlights the importance of SOC modelling in the context of LU in LCA, which is usually disregarded, as SOC is considered only in the context of land use change (LUC).