Although roots are an important source of soil organic matter (SOM) and are thought to be the major constituent of the particulate organic matter (POM) fraction, few studies have documented the fate of belowground C inputs in situ. The main purpose of this experiment was to determine the fate of root‐derived C vs. shoot‐derived C and to identify factors contributing to any differences in the retention of aboveground vs. belowground C inputs. We labeled hairy vetch (Vicia villosa Roth subsp. villosa) in situ with 13CO2 and followed both root‐ and shoot‐derived C in total soil organic C (SOC) and labile C pools for the first growing season following hairy vetch incorporation. At the end of the growing season, nearly one‐half of the root‐derived C was still present in the soil, whereas only 13% of shoot‐derived C remained. A greater proportion of root‐derived C was found as occluded POM and associated with the clay and silt fraction. Greater root‐derived C also was retained as chloroform‐extractable microbial biomass. We suggest that three different mechanisms contributed to the increased retention of root‐derived C: (i) the greater biochemical recalcitrance of root litter, (ii) increased physical protection of root‐derived POM within aggregates, and (iii) the continuous nature of root C inputs from exudates and fine root turnover. We conclude that shoot residues are broken down rapidly and serve as the source of N for the following cash crop, whereas the root litter is probably largely responsible for the short‐term soil structural improvements associated with the use of green manures. Furthermore, on the basis of these findings, we hypothesize that the greater retention of root‐derived C in the first 6 mo of decomposition will increase the persistence of this C in SOM in the long term.