We analyse how Earth system models represent vegetation carbon flux variability in the Amazon. By assessing environmental factors influencing vegetation, we identified CO₂ fertilization, photosynthetic sensitivity to solar radiation and heterotrophic respiration as key sources of model uncertainty under climate change. We also identified a stronger El Niño–Southern Oscillation (ENSO)-driven temperature impact under global warming. Reducing these uncertainties will enhance the reliability of tropical carbon–climate projections.