Root diseases are known to suppress forest regeneration and reduce growth rates, and they may become more common as susceptible tree species become maladapted in parts of their historic ranges due to climate change. However, current ecosystem models do not track the effects of root disease on net productivity, and there has been little research on how the dynamics of root disease affect carbon (C) storage and productivity across infected landscapes. We compared the effects of root disease against the effects of other types of forest disturbance across six national forest landscapes, 1990–2011. This was enabled by a monitoring tool called the Forest Carbon Management Framework (ForCaMF), which makes use of ground inventory data, an empirical growth model, and time series of Landsat satellite imagery. Despite several large fires that burned across these landscapes during the study period, retrospective ForCaMF analysis showed that fire and root disease had approximately equal impacts on C storage. Relative to C accumulation that would have occurred in their absence, fires from 1990 to 2011 were estimated to reduce regionwide C storage by 215.3 ± 19.1 g/m2 C, while disease in the same period was estimated to reduce storage by 211.4 ± 59.9 g/m2 C. Harvest (75.5 ± 13.5 g/m2 C) and bark beetle activity (14.8 ± 12.5 g/m2 C) were less important. While long-term disturbance processes such as root disease have generally been ignored by tools informing management of forest C storage, the recent history of several national forests suggests that such disturbances can be just as important to the C cycle as more conspicuous events like wildfires.