Plant responses to atmospheric CO2 enrichment, particularly above- vs. belowground allocation of net primary production (NPP), will affect soil organic matter (SOM) dynamics and stocks. Here we address mechanisms responsible for increased belowground C storage at the sweetgum FACE experiment at Oak Ridge National Laboratory. Plant C fixed under elevated CO2 was traced into free and microaggregated particulate organic matter (POM) and silt plus clay associated C using stable isotopes and alkaline CuO-extractable biopolymers (i.e. lignin phenols and aliphatic biopolymer substituted fatty acids-SFA). Ratios of syringyl to vanillyl and cinnamyl to vannillyl lignin phenols indicated that root-derived lignin was quantitatively more important than foliar-derived lignin, and that lignin in all fractions has become more root-like after 5 y of CO2 enrichment. This increase in root lignin was also associated with 13C depletion of all soil fractions, as a result of inputs of C fixed under the 13C-depleted elevated CO2, as well as C accrual in all soil fractions but microaggregated silt and clay. Sweetgum leaf litter and roots had distinct molecular signatures in their relative abundances of octadecyl and hexadecyl-SFA, allowing us to track their relative contributions to SOM. In contrast with lignin analyses, the SFA content of both coarse and fine POM was apparently dominated by leaf cutin rather than root suberin. However, consistent with lignin analyses, both fractions showed progressive enrichment with root input (suberin) as a result of increased root growth in the elevated-CO2 treatment. These results documenting enhanced root biopolymer retention lend further support to the hypothesis that allocation patterns under elevated CO2 have shifted towards greater delivery of C directly to the soil matrix where the potential for soil C accrual is increased, and confirm that changes in plant allocation patterns can have significant impacts on SOM dynamics and stabilization.