Nitrogen (N) supply in stockless organic farming may be improved through use of grass-clover for anaerobic digestion, producing biogas and digested manure for use as fertilizer in the crop rotation. We studied the effects of grass-clover management on N cycling, nitrous oxide (N2O) emissions and cash-crop yields in an organic arable crop rotation on a sandy loam soil in a cool temperate climate. The four-course crop rotation included spring barley (with undersown grass-clover), grass-clover, potato and winter wheat (with undersown cover crop). Two fertilization treatments were compared: “−M” where plant material from grass-clover cuts was left in the field to decompose and no fertilizer or manure was applied to any crop in the rotation; and “+M” where plant material from grass-clover cuts was harvested and equivalent amounts of N in digested manure used for fertilization of cash crops in the rotation (spring barley, potato and winter wheat); actual digestion of grass-clover cuttings was not possible, instead digested pig manure was used as substitute for digested grass-clover. Nitrous oxide fluxes were monitored between April 2008 and May 2009. In general, application of digested manure had little or no effect on N2O emissions. Periods of high N2O emissions coincided with cover crop and grass-clover residue turnover, with little added effect of digested manure application. Annual N2O emissions did not vary between fertilization treatments, but the +M treatment had cash crop dry matter yields that were 14% higher than in the −M treatment, and cash crop N yields were increased by 40%. The results show that reallocation of nutrients from grass-clover to cash crops following anaerobic digestion can help solve problems with low N availability. However, issues remain regarding N2O from cover crops and grass-clover in spring.