Biofuels have been proposed as environmentally benign substitutes to fossil fuels. There is, however, substantial uncertainty in the scientific literature about how an expanding bioenergy sector would interact with other land uses and what could be the environmental consequences. In the particular case of greenhouse gas balance, the magnitude of discrepancy is tremendously high among different studies. Such controversy has been often attributed to the way the co-products generated were accounted for. It is likely that the intensification of bioenergy production will lead to an increased input of these co-products to the soil as alternative amendments or fertilizers. However, limited research has been done to determine how this will influence microbial transformation processes in soil and thereby the emissions of greenhouse gases. Neither have related issues such as the stabilization of soil organic matter, soil structure and soil fertility been adequately studied. Here, we report a laboratory study on the effects of the application of bioenergy residues on C and N mineralization and greenhouse gas emissions in an agricultural soil. Ten co-products were selected from different energy sectors: anaerobic digestion (digestates), first generation biofuel residues (rapeseed meal, distilled dried grains with solubles), second generation biofuel residues (non-fermentables from hydrolysis of different lignocellulosic materials) and pyrolysis (biochars). They were added at the same N rate (150 kg N ha-1) to a moist (80% water filled pore space) sandy soil and incubated at 20 C for 60 days. Most residues followed fast mineralization dynamics with a flush of CO2 respiration within the first week. The biochars were the exception: they showed very low respiration rates. After 60 days, first generation biofuel residues had emitted more than 80% of added C as CO2. Around 60% was emitted in the case of second generation biofuel residues and 40% with digestates. Biochars were the most stable residues with the lowest CO2 loss between 0.5 and 5.8 % of total added C. Regarding N2O emissions, first generation biofuel residues led to the highest total N2O emissions (between 2.5 - 6.0% of added N). Second generation biofuel residues emitted between 1.0-2.0% of added N, whereas anaerobic digestates led to emissions lower than 1% of added N. The two biochars used in this study led to negative N2O emissions, i.e. lower than the blank soil. We conclude that, at least in the short term, the effects of biofuel residues on the combined greenhouse gas balance of the soil ranges from beneficial (biochar) via mixed (digestates, second generation biofuels) to manifestly detrimental (first generation biofuels). These effects should be taken into account in life cycle analyses of biofuel production.