Boreal regions store large quantities of carbon but are increasingly vulnerable to carbon loss due to disturbance and climate warming. The boreal region, underlain by discontinuous permafrost, presents a challenging landscape for itemizing current and potential carbon sources and sinks in the boreal soil and vegetation. The roles of fire, forest succession, and the presence (or absence) of permafrost on carbon cycle, vegetation, and hydrologic processes have been the focus of multidisciplinary research in this area for the past 20 years. However, projections of a warming future climate, an increase in fire severity and extent, and the potential degradation of permafrost could lead to major landscape process changes over the next 20 to 50 years. This provides a major challenge for predicting how the interplay between land management activities and impacts of climate warming will affect carbon sources and sinks in Interior Alaska. To assist land managers in adapting and managing for potential changes in the Interior Alaska carbon cycle we developed this review paper incorporating an overview of the climate, ecosystem processes, vegetation types, and soil regimes in Interior Alaska with a focus on ramifications for the carbon cycle. Our objective is to provide a synthesis of the most current carbon storage estimates and measurements to support policy and land management decisions on how to best manage carbon sources and sinks in Interior Alaska. To support this we have surveyed relevant peer reviewed estimates of carbon stocks in aboveground and belowground biomass for Interior Alaska boreal ecosystems. We have also summarized methane and carbon dioxide fluxes from the same ecosystems. These data have been converted into the same units to facilitate comparison across ecosystem compartments. We identify potential changes in the carbon cycle with climate change and human disturbance including how compounding disturbances can affect the boreal system. Finally, we provide recommendations to address the challenges facing land managers in efforts to manage carbon cycle processes. The results of this study can be used for carbon cycle management in other locations within the boreal biome which encompass a broad distribution from 45° to 83° north.