Digestate from biogas plants can play important role in agriculture by providing nutrients, improving soil structure and reducing the use of mineral fertilizers. Still, less is known about greenhouse gas emissions from soil during and after digestate application. The aim of the study was to estimate the emissions of carbon dioxide (CO2) and methane (CH4) from a field which was fertilized with digestate. The gas fluxes were measured with the eddy covariance system. Each day, the eddy covariance system was installed in various places of the field, depending on the dominant wind direction, so that each time the results were obtained from an area where the digestate was distributed. The results showed the relatively low impact of the studied gases emissions on total greenhouse gas emissions from agriculture. Maximum values of the CO2 and CH4 fluxes, 79.62 and 3.049 μmol s-1 m-2, respectively, were observed during digestate spreading on the surface of the field. On the same day, the digestate was mixed with the topsoil layer using a disc harrow. This resulted in increased CO2 emissions the following day. Intense mineralization of digestate, observed after fertilization may not give the expected effects in terms of protection and enrichment of soil organic matter.