This article examines how climate variability and ecological disturbances affect ecosystem composition and functioning in the Amazon region. We use a terrestrial ecosystem model, IBIS, and vary the treatment of climate (using either long-term average climate, or actual historical variations in climate) and disturbances (with uniform disturbance rates applied through the region). Interannual climate variability and frequent disturbances both favor grasses over trees, causing large increases in the geographic extent of savanna in the south and east of the region. A more constant climate and less frequent disturbances both favor trees over grasses, causing forest to dominate most of the study area. While climate variability and disturbances have a major impact on ecosystem structure, we find that compensating processes between herbaceous and woody plants damp the simulated response of carbon and water fluxes. Nevertheless, the cumulative impact of these changes in vegetation structure results in significant changes in soil and vegetation carbon stocks (up to 36%).