Slurry, farmyard manure and poultry manure are an inevitable consequence of livestock products generated from housed animals. These manures are recycled back to land for plants to use the nutrients they contain. However, since they contain inorganic N, microbially available sources of C and water, they provide the essential substrates required for the microbial production of N2O and CH4. These greenhouse gases can be produced and emitted at each stage of the ‘manure management continuum’, being the livestock building, manure stores, manure treatment and manure spreading to land. The contribution that manure management makes to total national agricultural emissions of N2O and CH4 vary, but can exceed 50% in countries reporting to the UNFCCC in 2009. On farm management decisions interact with environmental controls such as temperature and water availability of key microbial processes (i.e., nitrification, denitrification, methanogenesis, CH4 oxidation), affecting the magnitude of emissions from each stage of the manure management continuum. We review the current understanding of how manure management influences direct and indirect N2O emissions and CH4 emissions, introduce new data comparing direct N2O emissions following spreading of a range of manure types by different methods, and highlight some of the mitigations being considered by researchers and policy makers in developed and developing countries.