Woody encroachment of grasslands is a common phenomenon worldwide, but the consequences of this encroachment for ecosystem carbon storage, particularly belowground are not clear. We quantified total ecosystem carbon in the 3 major natural upland vegetation communities (grassland, shrubland, and forest) at the northern edge of the North American Great Plains. Total ecosystem carbon storage was significantly greater in forest (125.3 mg C·ha^-1) than in shrubland (92.4 mg C·ha^-1) or grassland (80.7 mg C·ha^-1), and this difference was due mainly to greater aboveground biomass, coarse root biomass, and the presence of a humus layer in the forest. Fine and total root biomass were also greater in forest than shrubland or grassland. In contrast, soil carbon was significantly greater in shrubland (80.6 mg C·ha^-1) and grassland (75.4 mg C·ha^-1) than in forest (48.6 mg C·ha^-1). We also investigated whether aboveground variables could be used to predict belowground carbon pools. Soil carbon increased significantly with aboveground herbaceous biomass, while fine root biomass increased with foliar biomass, but the strongest relationship was between total root biomass and total aboveground biomass (r² = 0.785). These are simple and effective predictors of belowground carbon pools. The rapid shift in carbon storage with forest encroachment, from being dominated by soil carbon in grassland to woody vegetation in forest, represents a significant change in ecosystem structure with implications for the carbon budget.