While intrinsic factors such as tree competition and soil nutrients have commonly been proposed to explain the observed patterns of tree mortality in Amazonia, we show in this study that windthrows act as important exogenous contributors to those observed patterns. Windthrows are more frequent in areas with no dry season, but are spatially and temporally variable across the basin. Regionally, Northwestern Amazonia (NWA) is more vulnerable to windthrows than Central Amazonia (CA). More frequent and severe convective storms in combination with soil characteristics in NWA may explain this vulnerability. In a demographic model using observed rates of tree mortality of 1% in CA and ~2% in NWA, we confirmed higher productivity but lower biomass in NWA compared to CA, primarily through forest composition and higher disturbance. Over the next century, projected increases in extreme rainfall events may produce a dramatic increase in windthrows across the basin. Our modeling results suggest that species composition in CA is more sensitive to a doubling of mortality rates than in NWA, leading to a larger decrease in biomass in CA. Our study emphasizes the importance of including exogenous factors in model simulations for reliable predictions of the carbon cycle.