Accurate characterization of Carbon (C) consequences of forest disturbances and management is critical for informed climate mitigation and adaptation strategies. While research into generalized properties of the forest C cycle informs policy and provides abstract guidance to managers, most management occurs at local scales and relies upon monitoring systems that can consistently provide C cycle assessments that explicitly apply to a defined time and place. We used an inventory-based forest monitoring and simulation tool to quantify C storage effects of actual fires, timber harvests, and forest regeneration conditions in the Greater Yellowstone Ecosystem (GYE). Results show that (1) the 1988 fires had a larger impact on GYE’s C storage than harvesting during 1985-2011; (2) continuation of relatively high harvest rates of the region’s National Forest land, which declined after 1990, would have shifted the disturbance agent primary importance on those lands from fire to harvest; and (3) accounting for local heterogeneity of post-disturbance regeneration patterns translates into large regional effects on total C storage. Large fires in 1988 released about 8.3 ± 0.3 Mg/ha of C across Yellowstone National Park (YNP, including both disturbed and undisturbed area), compared with total C storage reductions due to harvest of about 2.3 ± 0.3 Mg/ha and 2.6 ± 0.2 Mg/ha in adjacent Caribou-Targhee and Gallatin National Forests, respectively, from 1985-2011. If the high harvest rates observed in 1985-1989 had been maintained through 2011 in GYE National Forests, the C storage effect of harvesting would have quintupled to 10.5 ± 1.0 Mg/ha, exceeding the immediate losses associated with YNP’s historic fire but not the longer-term net loss of carbon (16.9 ± 0.8 Mg/ha). Following stand-replacing disturbance such as the 1988 fires, the actual regeneration rate was slower than the default regional average rate assumed by empirically calibrated forest growth models. If regeneration following the 1988 fire had reached regionally average rates, either through different natural circumstances or through more active management, YNP would have had approximately 4.1 Mg/ha more forest carbon by year 2020. This study highlights the relative effects of fire disturbances and management activities on regional C storage, and demonstrates a forest carbon monitoring system that can be both applied consistently across the US and tailored to questions of specific local management interest.