Cover cropping is a key agro-environmental measure in Europe. Cover crops may reduce N2O emissions by reducing soil nitrate content, while easily decomposable residues can enhance greenhouse gas losses. In a field study, emissions from the cover cropped fields compared to the fallow at two climatically different sites (semi-arid vs. humid) in Austria were measured with closed chambers and different driving factors were studied. The height of post-cover crop emissions was compared to gaseous losses during the management operations in the subsequent main crop maize. N2O and CO2 emissions following the cover crops were low even at high emission moments compared to the losses induced by the main crop management operations. Highest risk of N2O losses was from mustards due to low C/N ratio and possibly as a consequence of glucosinolate decomposition. CO2 emissions in the cover cropped plots were generally higher compared to the fallow, indicating an enhanced soil microbiological activity. Dissolved organic carbon was found as a sensitive indicator related to the greenhouse gas emissions. We concluded that the environmental benefits from cover cropping are not achieved at the cost of an enhanced greenhouse gas emission and that pure stands of late sown brassica cover crops should be avoided to prevent any risk of increased N2O losses.