Cover crops (CC) can contribute to climate protection as a result of their effects on soil nitrogen (N) cycling and nitrous oxide (N2O) emission and by increasing soil organic carbon (SOC) stocks. This study explored the influence of different winter CC (saia oat, winter rye and spring vetch) compared with bare fallow, followed by silage maize on N2O emissions and soil mineral N (SMN) dynamics, as well as on SOC stocks in year-round replicated field plot experiments in four fields located at two sites in northern Germany (Kiel, Uelzen) over two consecutive years (2018/19 and 2019/20). Non-legume CC decreased SMN contents in 0–30 cm during the CC period, but this did not result in decreased cumulative N2O emissions over that time. Decreased emissions during CC growth were offset by increased emissions during CC mineralisation after frost and incorporation. Higher cumulative N2O emissions during the maize period in all CC treatments compared with bare fallow (significant for non-legume CC) indicated that the incorporated CC biomass still boosted N2O emissions under the following crop. Overall, including CC in the cropping system increased annual and yield-related N2O emissions compared with bare fallow (significant only for non-legumes). The increase in annual N2O emissions of 0.84 ± 1.06 kg N2O-N ha−1 yr−1 was only partly offset by the estimated mitigation potential for indirect N2O emissions of 0.52 ± 0.14 kg N2O-N ha−1 yr−1. The mean annual increase in SOC induced by growing CC every fourth year over a 50-year period was 40–60 kg C ha−1 yr−1. In summary, CC had both positive and negative effects on greenhouse gas exchange. Site and crop rotation optimised CC systems, and a more precise and site-specific consideration of fertilising effects might help improve the net greenhouse gas budget of CC.