Agricultural waste contributes significantly to greenhouse gas (GHG) emissions if not adequately recycled and sustainably managed. A recurring agricultural waste is livestock waste that has consistently served as feedstock for biogas systems. The objective of this study was to assess the use of animal waste digestate to mitigate GHG emissions in agricultural fields. Wheat (Triticum spp. L.) was fertilized with different types of animal waste digestate (organic fertilizers) and synthetic nitrogen fertilizer (inorganic fertilizer). The 170 kg N/ha presented in digestates were split fertilized at an application rate of 90 and 80 kg N/ha. Emissions of GHGs (carbon dioxide (CO2), methane (CH4) and nitrous oxide (N2O)) were monitored directly by a static chamber system. The soil and environmental variables were measured to determine their influence on GHG emissions. Emission peaks in N2O and CO2 after the first application of fertilizers with the emissions flattening out over the cultivating season while CH4 emission was negligible with no apparent patterns observed. Results showed individual and cumulative emissions of CO2, CH4 and N2O from the digestates were relatively low and digestate fertilization could be an efficient method for reducing GHGs from agricultural sources in temperate climate conditions.