Cover crops are increasingly used for biogas production, a renewable energy source, without competing for food production. The behavior of the resulting digestates after soil application is poorly understood, which prevents their efficient recycling in agriculture and the environmental assessment of their application. The objective of this study was to quantify the nitrogen availability and potential carbon storage of cover crop-issued digestates after soil application. A total of 10 raw digestates, 2 liquid phases, and 3 solid phases after phase separation were sampled. Main cover crops used in the sampled biogas plants were winter barley, rye, and maize. Classical physicochemical analyses and laboratory incubations to study their C and N mineralization were conducted. Despite a moderate C mineralization of raw and liquid digestates after 91 days, their initial limited carbon content induced, in the end, a low contribution to soil organic carbon (13 and 11 kg remaining C Mg-1 FM, respectively), similar to a pig slurry and much lower than a bovine manure. With a higher initial carbon content and lower C mineralization, the contribution of solid digestates to carbon storage could be higher if applied at a sufficient rate. Organic N mineralization of raw and liquid digestates was moderate, but their N availability was high (3 and 4 kg available N Mg-1 FM, respectively), thanks to their mineral nitrogen contents, similar again to a pig slurry. In contrast, that of solid digestate was almost null with a very low mineral N content and no organic N mineralization. Finally, all the digestates also brought significant amounts of P and K.