Many current organic arable agriculture systems are challenged by a dependency on imported livestock manure from conventional agriculture. At the same time organic agriculture aims at being climate friendly. A life cycle assessment is used in this paper to compare the carbon footprints of different organic arable crop rotations with different sources of N supply. Data from long-term field experiments at three different locations in Denmark were used to analyse three different organic cropping systems (‘Slurry’, ‘Biogas’ and ‘Mulching’), one conventional cropping system (‘Conventional’) and a “No input” system as reference systems. The ‘Slurry’ and ‘Conventional’ rotations received slurry and mineral fertilizer, respectively, whereas the ‘No input’ was unfertilized. The ‘Mulching’ and ‘Biogas’ rotations had one year of grass-clover instead of a faba bean crop. The grass-clover biomass was incorporated in the soil in the ‘Mulching’ rotation and removed and used for biogas production in the ‘Biogas’ rotation (and residues from biogas production were simulated to be returned to the field). A method was suggested for allocating effects of fertility building crops in life cycle assessments. The results showed significantly lower carbon footprint of the crops from the ‘Biogas’ rotation (assuming that biogas replaces fossil gas) whereas the remaining crop rotations had comparable carbon footprints per kg cash crop. The study showed considerable contributions caused by the green manure crop (grass-clover) and highlights the importance of analysing the whole crop rotation and including soil carbon changes when estimating carbon footprints of organic crops especially where green manure crops are included. •Carbon footprints of crops from organic and conventional crop rotations were assessed.•The contributions caused by the green manure crop were considerable.•Highlights the importance of analysing the whole crop rotation and to include soil carbon changes.•Carbon footprint of organic compared to conventional varied depending on production practice.•Indicates a potential for improving the carbon footprint of organic produce.