Biogas residues contain valuable plant nutrients, important to the crops and also to soil microorganisms. However, application of these materials to the soils may contribute to the emission of greenhouse gases (GHG) causing global warming and climate change. In the present study, incubation experiment was carried out, where the emission rates of N2O and CH4 were measured after amending two soils with two types of biogas residues: (1) a regular residue from a large scale biogas plant (BR) and (2) a residue from an ultrafiltration membrane unit connected to a pilot-scale biogas plant (BRMF). The emissions of N2O and CH4 were measured at two occasions: at 24 h and at 7 days after residue amendment, respectively. Amendment with filtered biogas residues (BRMF) led to an increase in N2O emissions with about 6-23 times in organic and clay soil, respectively, in comparison to unfiltered biogas residues (BR). Methane emission was detected in small amounts when filtered biogas residue was added to the soil. Amendment of unfiltered biogas to the organic soil resulted in net consumption. In conclusion, fertilization with BRMF can be combined with risk of an increase N2O emission, especially when applied to organic soils. However, in order to transfer these results to real life agriculture, large scale field studies need to be carried out