FIRESUM, an ecological process model incorporating surface fire disturbance, was modified for use in southwestern ponderosa pine ecosystems. The model was used to determine changes in forest structure over time and then applied to simulate changes in aboveground biomass and nitrogen storage since exclusion of the natural frequent fire regime in an unharvested Arizona forest. Dendroecological reconstruction of forest structure in 1876, prior to Euro-American settlement, was used to initialize the model; projections were validated with forest measurements in 1992. Biomass allocations shifted from herbaceous plants to trees, and nitrogen was increasingly retained in living and dead tree biomass over the 116-year period (1876–1992). Forest conditions in 1992 were substantially degraded compared to reference presettlement conditions: old-growth trees were dying at accelerated rates, herbaceous production was reduced nearly 90%, and the entire stand was highly susceptible to high-intensity wildfire. Following an experiment initiated in 1993 to test ecological restoration treatments, future changes were modeled for the next century. Future forest structure remained within the natural presettlement range of variability under the full restoration treatment, in which forest biomass structure was thinned to emulate presettlement conditions and repeated low-intensity fire was reintroduced. Simulation of the control treatment indicated continuation of exceptionally high tree density, probably culminating in stand-replacing ecosystem change through high-intensity wildfire or tree mortality from pathogens. Intermediate results were observed in the partial restoration treatment (tree thinning only); the open forest structure and high herbaceous productivity found immediately after treatment were gradually degraded as dense tree cover reestablished in the absence of fire. Modeling results support comprehensive restorative management as a long-term approach to conservation of key indigenous ecosystem characteristics.