Recently, the Swedish government has set up the target that 20% of the total arable land in Sweden shall be managed according to the principles of “ecological agriculture”. This will have implications on long-term soil carbon stocks and soil fertility. To maintain agricultural production at the present level, an increase in “ecological” farming practices will probably result in an increased total area used for arable production. In regions with high livestock densities, the area used for perennial leys will increase, which probably will lead to increased carbon stocks in these soils. On the other hand, lower yields in cereals will result in lower carbon stocks and increase the demand for arable land used for grain production. Thus, the area that potentially is available for energy and/or fibre production will decrease. To elucidate the total effect of the 20% target on Swedish soil carbon stocks in a 30-year perspective, we use a dynamic soil carbon model (Andrén & Kätterer, 1997; Ecol. Appl. 7:1226-1236). This model has been calibrated for a number of long-term experiments and is used in the Swedish land use change reporting systems according to the Kyoto protocol. We present the outcomes from one scenario with the boundary conditions that the amount of agricultural and livestock products are unchanged within each of the eight agricultural regions and that the surplus area under intensive production is used for energy production (grasses and short-rotation forests). Socio-economic consequences of this change in management are not considered. We estimate that about 5% of soil carbon (or about 15 Mton) would be lost from Swedish agricultural soils during a 30-year period after changing management according to the principles of “ecological agriculture”.