The use of anaerobic digestates as fertilizer is proposed as a means to close agricultural nutrient cycles. However, digestates have higher inorganic nitrogen contents than raw manures, which could translate into increased emissions of potent greenhouse gases such as nitrous oxide (N2O) and methane (CH4). To mitigate these emissions, the addition of biochar with high nutrient absorption capacity is suggested. To quantify the effects of anaerobic digestion and biochar amendment on N2O and CH4 emissions, we conducted a study over 33 months with four different crops (silage maize, winter wheat, winter barley, and forage grass). We measured soil parameters such as mineral nitrogen, moisture, and temperature. The N2O emissions after application of digestates were generally similar to those observed after cattle slurry or mineral fertilizer application. The highest N2O emissions were observed in the first year of the experiment during maize cultivation and were strongly influenced by high soil nitrate concentrations, which were likely linked to enhanced soil organic N mineralization after ley termination. The CH4 emissions were mostly negative. The addition of biochar to co-digested manure before application at an annual rate of 2 t ha− 1 had no effect on N2O emissions but led to short-lived CH4 peaks from organic fertilizers directly after spreading. We conclude that digestates do not promote larger N2O emissions than mineral fertilizers or cattle slurry, and that biochar addition to digestates in small application quantities does not reduce N2O emissions but bears the risk of CH4 release.