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The effects of climate changes on biotic expansion or divergence is a widely debated topic. This discussion is particularly relevant for northern Amazonia where patches of open vegetation environments that harbor high endemic and specialized species are present in a matrix of tall closed canopy forest. This paper presents the depositional chronology and evolution of an 8.7-m thick stabilized fluvial and eolian sediment profile in a sandy plain substrate that underpins the largest open vegetation enclave in northern Amazonia. Three depositional units were identified using optically stimulated luminescence and radiocarbon ages coupled with grain size, magnetic susceptibility, and reflectance analyses. A lower unit of coarse fluvial silt deposited between 53 and 28 ka is overlain unconformably by a 5-m thick middle unit of fine eolian sand deposited at high accumulation rates between the Last Glacial Maximum (23-19 ka) and Heinrich Stadial 1 (HS1; 18.1-14.7 ka) when persistent and long-lasting shifts of the Intertropical Convergence Zone (ITCZ) to the Southern Hemisphere promoted dry and windy conditions in northern South America. An upper similar to 2-m thick unit was deposited when the climate became wetter after HS1, promoting the formation of soils that support open vegetation habitats. This study indicates that abrupt millennial-scale climate events can induce significant changes in the Amazonian landscape, which in turn play an essential role in the distribution and diversification of specialized biota.