Organic farming (OF) principles include the idea of reducing dependence of fossil fuels, but little has been achieved on this objective so far in Danish OF. Energy use and greenhouse gas (GHG) emissions from an average 39 ha cash crop farm were calculated and alternative crop rotations for bio-energy production were modeled. Growing rapeseed on 10% of the land could produce bio-diesel to replace 50–60% of the tractor diesel used on the farm. Increasing grass-clover area to 20% of the land and using half of this yield for biogas production could change the cash crop farm to a net energy producer, and reduce GHG emissions while reducing the overall output of products only marginally. Increasing grass-clover area would improve the nutrient management on the farm and eliminate dependence on conventional pig slurry if the biogas residues were returned to cash crop fields.