Livestock farming systems are major sources of trace gases contributing to emissions of the greenhouse gases (GHG) nitrous oxide (N2O) and methane (CH4), i.e. N2O accounts for 10% and CH4 for 30% of the anthropogenic contributions to net global warming. This paper presents scenario assessments of whole-system effects of technologies for reducing GHG emissions from livestock model farms using slurry-based manure management. Changes in housing and storage practice, mechanical separation, and incineration of the solid fraction derived from separation were evaluated in scenarios for Sweden, Denmark, France, and Italy. The results demonstrated that changes in manure management can induce significant changes in CH4 and N2O emissions and carbon sequestration, and that the effect of introducing environmental technologies may vary significantly with livestock farming practice and interact with climatic conditions. Shortening the in-house manure storage time reduced GHG emissions by 0–40%. The largest GHG reductions of 49 to, in one case, 82% were obtained with a combination of slurry separation and incineration, the latter process contributing to a positive GHG balance of the system by substituting fossil fuels. The amount and composition of volatile solids (VS) and nitrogen pools were main drivers in the calculations performed, and requirements to improve the assessment of VS composition and turnover during storage and in the field were identified. Nevertheless, the results clearly showed that GHG emission estimates will be unrealistic, if the assumed manure management or climatic conditions do not properly represent a given country or region. The results also showed that the mitigation potential of specific manure management strategies and technologies varied depending on current management and climatic conditions.