With growing interest in wood bioenergy there is uncertainty over greenhouse gas emissions associated with offsetting fossil fuels. Although quantifying postharvest carbon (C) fluxes will require accurate data, relatively few studies have evaluated these using field data from actual bioenergy harvests. We assessed C reductions and net fluxes immediately postharvest from whole-tree harvests (WTH), bioenergy harvests without WTH, and nonbioenergy harvests at 35 sites across the northeastern United States. We compared the aboveground forest C in harvested with paired unharvested sites, and analyzed the C transferred to wood products and C emissions from energy generation from harvested sites, including indirect emissions from harvesting, transporting, and processing. All harvests reduced live tree C; however, only bioenergy harvests using WTH significantly reduced C stored in snags (P < 0.01). On average, WTH sites also decreased downed coarse woody debris C while the other harvest types showed increases, although these results were not statistically significant. Bioenergy harvests using WTH generated fewer wood products and resulted in more emissions released from bioenergy than the other two types of harvests, which resulted in a greater net flux of C (P < 0.01). A Classification and Regression Tree analysis determined that it was not the type of harvest or amount of bioenergy generated, but rather the type of skidding machinery and specifics of silvicultural treatment that had the largest impact on net C flux. Although additional research is needed to determine the impact of bioenergy harvesting over multiple rotations and at landscape scales, we conclude that operational factors often associated with WTH may result in an overall intensification of C fluxes. The intensification of bioenergy harvests, and subsequent C emissions, that result from these operational factors could be reduced if operators select smaller equipment and leave a portion of tree tops on site.