Predictions of the magnitude and timing of leaf phenology in Amazonian forests remain highly controversial, which limits our understanding of future ecosystem function with a changing environment. Here, we use biweekly terrestrial LiDAR surveys spanning wet and dry seasons in Central Amazonia to show that plant phenology of old-growth forests varies strongly across strata but that this seasonality is sensitive to disturbances arising from forest fragmentation. In combination with continuous microclimate measurements, we found that when maximum daily temperatures reached 35 °C in the latter part of the dry season, the upper canopy of large trees in undisturbed forests shed their leaves and branches. By contrast, the understory greens-up with increased light availability driven by the upper canopy loss alongside more sunlight radiation, even during periods of drier soil and atmospheric conditions. However, persistently high temperatures on forest edges exacerbated the upper canopy losses of large trees throughout the dry season, and the understory seasonality in these light-rich environments was disrupted as a result of the altered canopy structure. These findings demonstrate the plant-climate interactions controlling the seasonality of wet Amazonian forests and show that forest fragmentation will aggravate forest loss under a hotter and drier future scenario.