Greenhouse gas emission from liquid livestock manure storage is a considerable contributor to global warming and accurate farm-scale models for predicting emission are needed for estimating effects of manure management strategies. In this study we measured degradation of organic matter components of pig slurry with anaerobic and aerobic manure surface and at 10℃ and 20℃. Simultaneously, methane and carbon dioxide emission were measured and carbon emission from both anaerobic and aerobic processes was determined. Carbon dioxide loss due to surface respiration, did not limit methane emission during the incubation experiment at 10℃ and 20℃, but limited production of methane during subsequent anaerobic digestion at 38℃. Surface respiration rates varied between 10 - 80 g CO₂ m^-2 day^-1 and temperature dependent rate equations describing surface respiration was implemented in a farm-scale methane emission model (ABM). ABM simulations suggested that ca. 10% of carbon loss from typical slaughter pig barns and < 2% from outdoor pig manure storage was as carbon dioxide from surface respiration. Simulations also indicated that slurry filling level and seasonal variation in temperature considerably influenced methane to carbon dioxide emission ratio. This combined experimental and modelling study suggest that farm-scale models must reflect carbon loss from both aerobic and anaerobic process to accurately capture carbon emission dynamics and the farm-scale greenhouse gas emission.