Abstract For the economic evaluation of soil carbon sequestration and GHG mitigation in Swiss agriculture, we developed the Swiss INTegrated AGricultural ALlocation model (S_INTAGRAL). This is a recursive-dynamic linear optimization model which maximizes the aggregate annual income (labor income plus land rents) of Swiss agriculture under consideration of various constraints and dynamic properties of the system. It provides an analytical tool for economic analyses of GHG abatement strategies in the agricultural sector and to assess marginal GHG abatement costs. The model includes the most important activities of Swiss agriculture with regard to revenue, land use, livestock production and GHG emissions. It is divided into three major production zones (plains, hills and mountain area) and consists of the three production modules “livestock”, “grassland” and “cropland” that are integrated through the forage–manure cycle. With this integrated and recursive-dynamic formulation, the model does not have the extreme behavior which is characteristic for linear programming models. It provides an analytical tool for the assessment of future GHG emissions and mitigation costs from an agricultural system perspective.