The anaerobic digestion industry, which is still developing, generates biogas from organic waste products. A co-product of this process, digestate, is increasingly produced and can be recycled on agricultural land as an alternative to mineral fertilizers. Biogas digestate is a recent product whose chemical composition differs from that of its source material, and additional data still need to be acquired on its effects on dissolved carbon fluxes. The objectives of this study were to assess (i) the effects of applying biogas digestate on dissolved organic carbon (DOC) and dissolved inorganic carbon (DIC) fluxes with different winter crops, (ii) the dynamics of DOC and DIC concentrations during the drainage season, and (iii) the annual dynamics of DOC and DIC fluxes along the soil profile. The study examined effects of applying biogas digestate, pig slurry, or a mineral fertilizer to winter wheat and two catch crops (mustard and a multispecies crop) on DOC and DIC fluxes in the soil. Lysimeters at 40 cm (topsoil) and 90 cm (subsoil) depths were monitored from 2014 to 2023, from November to March (i.e., 9 winter drainage seasons). During the drainage season, the DOC concentration was highest with digestate, and its timing depended on development of the cover crop: from the beginning of the drainage season for mustard and the multispecies crop and around February for wheat. Applying digestate increased the topsoil DOC fluxes (mean of 35.7 ± 13.7 kg.ha 1 with digestate vs. 21.0 ± 6.7 kg.ha 1 with the other treatments), particularly under mustard. Topsoil DIC fluxes were highest with pig slurry due to higher mineralization than that with digestate (mean of 59.1 ± 22.8 kg.ha 1 with pig slurry vs. 46.2 ± 16.3 kg.ha 1 with the other treatments). In the subsoil, DOC fluxes were low (6.2 ± 4.1 kg.ha 1) and DIC fluxes were high (80.0 ± 45.7 kg.ha 1), with no difference among treatments