Greenhouse gas and ammonia emissions are important environmental impacts from manure management in the layer-hen industry. The present study aimed to quantify emissions of nitrous oxide (N2O), methane (CH4) and ammonia (NH3) from layer-hen manure stockpiles, and assess the use of an impermeable cover as an option to mitigate emissions. Gaseous emissions of N2O, CH4 and NH3 were measured using open-path FTIR spectroscopy and the emission strengths were inferred using a backward Lagrangian stochastic model. Emission factors were calculated from the relationship between gaseous emissions and stockpile inputs over a 32-day measurement period. Total NH3 emissions were 5.97 ± 0.399 kg/t (control) and 0.732 ± 0.116 kg/t (mitigation), representing an 88% reduction due to mitigation. Total CH4 emissions from the mitigation stockpile were 0.0832 ± 0.0198 kg/t. Methane emissions from the control and N2O emissions (control and mitigation) were below detection. The mass of each stockpile was 27 820 kg (control) and 25 120 kg (mitigation), with a surface area of ~68 m2 and a volume of ~19 m3. Total manure nitrogen (N) and volatile solids (VS) were 25.2 and 25.8 kg/t N, and 139 and 106 kg/t VS for the control and mitigation stockpiles respectively. Emission factors for NH3 were 24% and 3% of total N for the control and mitigation respectively. Methane from the mitigation stockpile had a CH4 conversion factor of 0.3%. The stockpile cover was found to reduce greenhouse gas emissions by 74% compared with the control treatment, primarily via reduced NH3 and associated indirect N2O emissions.