The aim of this study was to investigate the effect of three different dietary strategies on milk production and composition, enteric CH4 emissions, slurry storage losses of CH4 and total emissions of CH4 with and without biogas production. Fifty-four cows were allocated to three diets according to parity and days in milk. Two diets were based on maize silage with (MS+) or without (MS−) supplementation of crushed rapeseed, and the third diet was based on late cut grass silage without supplementation of crushed rapeseed (GS−). Dry matter intake, milk yield and composition were measured. Enteric methane emissions were measured on 24 cows by means of indirect calorimetry. Slurry was collected the last 10 days of the experiment. Ultimate biogas yield, CH4 emissions at different storage temperatures and yield in a thermophilic biogas digester were determined for the three slurries. Dry matter intake was 22.5 kg/day on MS− and MS+ which was significantly higher than the 20.7 kg/day on GS−. Yield of energy corrected milk (ECM) was 2.8 and 2.5 kg higher on MS+ compared with GS− and MS−, respectively. Enteric CH4 emissions related to dry matter intake or gross energy intake were highest for GS−. Supplementation of crushed rapeseed did not affect enteric CH4 emissions. Ultimate biogas yield and yield of CH4 in the digester were higher for MS+ and MS− than for GS−. Storage emissions from slurry increased with increasing storage temperature. The average total CH4 per kg ECM for the three treatments (mean±standard deviation) was 25.3±2.5, 26.8±3.3 and 29.0±4.2 L CH4/kg ECM if manure was stored at 10 °C, 15 °C or 20 °C, respectively. When the slurry was digested in a laboratory scale biogas plant, the lowest total CH4 emissions per kg ECM were observed for MS+ (20.5 L CH4/ECM) and the highest for GS− (24.3 L CH4/ECM) corresponding to the enteric emissions of CH4. It was found that MS+ had a higher yield and a lower milk fat concentration than MS− and GS−. Although MS+ had a lower milk fat concentration, the ECM yield was significantly higher for MS+ than for the two other diets. It was furthermore concluded that feed ration induced reductions in enteric methane emissions might be counteracted or complemented by changed methane emissions from slurry storage. The slurry biogas yield was highest (per kg ECM) from cows fed MS+ which also gave the lowest total methane emissions per kg ECM.