AbstractRemoving agricultural cellulosic residues from fields for the production of ‘second generation biofuels'has the potential to profoundly alter C and N cycling in soil, increasing the risk of soil organic matter depletion and favoring soil–atmosphere gaseous exchanges. However, these negative impacts could potentially be offset by amending the soil with the solid by‐product which is generated during bioethanol production. In a 100 days laboratory study, we investigated the fate of C and N after soil amendment with doubly labeled (13C, 15N) wheat residue (WR) and the corresponding bioethanol by‐product (i.e. nonfermentable wheat residue NFWR) with and without extra N addition. Substituting WR with the corresponding amount of recovered bioethanol by‐product partially compensated the C losses of full crop residue removal. When the equivalent amount of C was added as WR and NFWR, NFWR‐derived C was found in significantly higher proportion in macroaggregates in soil (17.0 vs. 8.9%) after 100 days. Addition of both WR and NFWR reduced soil organic C (SOC) mineralization, i.e. it caused a negative priming effect in soil. However, this pattern was reversed when extra N was added. Both WR and NFWR increased the proportion of soil water‐stable macroaggregates from 16% (in control) to 20–24% (in the different treatments). The results suggest that the more recalcitrant compounds derived from bioethanol production may stabilize more strongly and persist within the protected fractions of SOM pools. Our study demonstrates that NFWR, compared with WR application, neither increased N2O emissions nor had a negative impact on aggregate formation in the midterm. This demonstrates that NFWR has potential for replenishing SOC stocks.