Because forest ecosystems have the capacity to store large quantities of carbon (C), there is interest in managing forests to mitigate elevated CO2 concentrations and associated effects on the global climate. However, some mitigation techniques may contrast with management strategies for other goals, such as maintaining and restoring biodiversity. Forest thinning reduces C storage in the overstory and recruitment of detrital C. These C stores can affect environmental conditions and resource availability in the understory, driving patterns in the distribution of early and late-seral species. We examined the effects of replicated (N = 7) thinning experiments on aboveground C and understory vascular plant species richness, and we contrasted relationships between aboveground C and early- vs. late-seral species richness. Finally, we used structural equation modeling (SEM) to examine relationships among early- and late-seral species richness and live and detrital aboveground C stores. Six years following thinning, aboveground C was greater in the high-density treatment and untreated control than in moderate- (MD) and variable-density (VD) treatments as a result of reductions in live overstory C. In contrast, all thinning treatments increased species richness relative to controls. Between the growing seasons of years 6 and 11 following treatments, the live overstory C increment tended to increase with residual density, while richness decreased in MD and VD treatments. The richness of early-seral species was negatively related to aboveground C in MD and VD, while late-seral species richness was positively (albeit weakly) related to aboveground C. Structural equation modeling analysis revealed strong negative effects of live overstory C on early-seral species richness balanced against weaker positive effects on late-seral species richness, as well as positive effects of detrital C stocks. A trade-off between carbon and plant species richness thus emerges as a net result of these relationships among species traits, thinning treatments, and live and detrital C storage. Integrating C storage with traditional conservation objectives may require managing this trade-off within stands and landscapes (e.g., maintain early-seral habitat and species within dense, C-rich forests and, conversely, live and detrital C stores in early-seral habitats) or separating these goals across scales and species groupings.