Plant–microbe interactions in the rhizosphere shape carbon and nitrogen cycling in soil organic matter (SOM). However, there is conflicting evidence on whether these interactions lead to a net loss or increase of SOM. In part, this conflict is driven by uncertainty in how living roots and microbes alter SOM formation or loss in the field. To address these uncertainties, we traced the fate of isotopically labelled litter into SOM using root and fungal ingrowth cores incubated in a Miscanthus x giganteus field. Roots stimulated litter decomposition, but balanced this loss by transferring carbon into aggregate associated SOM. Further, roots selectively mobilized nitrogen from litter without additional carbon release. Overall, our findings suggest that roots mine litter nitrogen and protect soil carbon. Root and microbial processes in the rhizosphere shape soil organic matter (SOM) cycling, but conflicting rhizosphere processes can both enhance and reduce SOM retention. To address the resulting uncertainty, we followed litter decomposition and SOM formation as a function of root ingrowth and soil nutrient availability in a Miscanthus x giganteus field. We observed that roots transferred litter carbon into a more protected SOM pool and selectively mobilized nitrogen without additional carbon release, suggesting that roots efficiently mine nitrogen and protect soil carbon.