Cattle manure can be processed to produce bioenergy, resulting in by-products with different physicochemical characteristics. To evaluate whether application of such bioenergy by-products to soils would be beneficial compared with their unprocessed counterpart, we quantified differences in greenhouse gas emissions and carbon (C) and nitrogen (N) dynamics in soil. Three by-products (15N-labeled cattle manure, from which anaerobic digestate was obtained, which was subsequently pyrolysed) were applied to a loess and a sandy soil in a laboratory incubation study. The highest losses of soil C from biological activity (CO2 respiration) were observed in manure treatments (39% and 32% for loess and sandy soil), followed by digestate (31% and and 18%), and biochar (15% and and 7%). Emissions of nitrous oxide (N2O) ranged from 0.6% of applied N from biochar to 4.0% from manure. Isotope labeling indicated that manure N was most readily mineralized, contributing 50% to soil inorganic N. The anaerobic digestate was the only by-product increasing the mineral N pool, while reducing emissions of N2O compared with manure. In biochar treatments, less than 18.3% of soil mineral N derived from the biochar, while it did not constrain mineralization of native soil N. By-products of anaerobic digestion and pyrolysis revealed soil fertility in addition to environmental benefits. However, the reported advantages lessen when the declining yields of C and N over the bioenergy chain are considered.