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We assessed the impact of western juniper (Juniperus occidentalis) encroachment and removal on C pools in a semi-arid sagebrush ecosystem. We used spatially-intensive sampling to create sub-canopy estimates of surface soil C (0–10 cm depth) and litter C pools that consider variation in tree size/age and sub-canopy location for live juniper and around stumps that were cut 7 years prior to sampling. We coupled the present size distribution of junipers with extensive existing allometric information about juniper in this region to estimate how landscape-level C pools would change through time under future management and land cover scenarios. Juniper encroachment and removal leads to substantial changes in C pools. Best-fit models for surface soil and litter C included positive responses to shrub basal diameter and negative responses to increasing relative distance from the bole to dripline. Juniper removal led to a net loss of surface C as a function of large decreases in litter C and small increases in surface soil C. At the landscape scale, deep soil C was the largest C pool (77 Mg C ha−1), with an apparent lack of sensitivity to management. Overall, encroachment led to substantial increases in C storage over time as juniper size increased (excluding deep soil C, ecosystem C pools increased from 13.5 to 30.2 Mg C ha−1 with transition from sagebrush-dominated to present encroachment levels). The largest pool of accumulation was juniper aboveground C, with important other pools including juniper roots, litter, and surface soil C. Woody encroachment and subsequent brush management can have substantive impacts on ecosystem C pools, although our data suggest the spatiotemporal patterns of surface C pools need to be properly accounted for to capture C pool responses. Our approach of coupling spatially-intensive surface C information with shrub distribution and allometric data is an effective method for characterizing ecosystem C pools, offering an opportunity for filling in knowledge gaps regarding woody encroachment and brush management impacts on local-to-regional ecosystem C pools.