Intensification of livestock production in many parts of the world has led to increasing atmospheric losses of N in connection with storage and field application of manure. Both types of emissions are influenced by manure organic matter content via mechanisms such as composting, crust formation, mineralization–immobilization turnover, and water retention. Manure management affects the potential for, and balance between, NH3 and N2O emissions. The interaction between NH3 and N2O may be positive (e.g., both emissions are reduced by an airtight cover during storage and stimulated by composting), or negative (e.g., direct N2O emissions from soil will potentially increase if losses of NH3 are prevented during storage or field application). Emissions of NH3 and N2O negatively affect N use efficiency and the greenhouse gas (GHG) balance of livestock production. Ammonia and N2O emissions and GHG balances of manure management, and the mitigation potential of individual and combined measures to prevent emissions, are calculated for dairy cattle with an emission factor approach. A more precise determination of overall N2O and NH3 emissions requires a model that accounts for the complex interactions between C and N transformations at each stage of the manure management chain in a time scale that is relevant for management practices such as retention time in housing and storage, treatment to optimize nutrient management, and timing of field application. Modelling emissions of N2O from field applied manure is a particular challenge due to the heterogeneity in distribution of O2 supply and O2 demand which is introduced.