Located at the transition between the Saharan and Sahelian zones, at the center of one of the largest endorheic basins, Lake Chad is ideally located to record regional environmental changes that occurred in the past. However, until now, no Holocene archive was directly cored in this lake. In this paper, we present pollen data from the first sedimentary sequence collected in Lake Chad (13° N; 14° E; Sahel region). Dated between ca. 6700 and ca. 5000 cal yr BP, this record is continuous and encompasses part of the termination of the African Humid Period (AHP). Vegetation reconstructions are based on standard analyses of pollen diagrams and are strengthened by quantitative approaches. Potential biomes are reconstructed using the biomization method and mean annual precipitation (Pann) is estimated using the modern analogues technique. Results show that, between ca. 6700 and ca. 6050 cal yr BP, a vegetation close to humid woodland or humid savanna, including elements currently found further southward, thrived in the vicinity of the Mega-Lake Chad in place of the modern dry woodland, steppe and desert vegetation. At the same time, montane forest populations extended further southward on the Adamawa Plateau. The high abundance of lowland humid pollen taxa, particularly of Uapaca, is interpreted as the result of a northward migration of the corresponding plants during the AHP. This preferential zonal occurrence of these taxa in Lake Chad Basin (LCB) (rather than extrazonal) is driven by more humid local and regional climate conditions at this latitude, as shown by mean Pann estimated values of ca. 800 ( 400/+700) mm during this period. However, we cannot rule out that an increase of the Chari–Logone inputs into the Mega-Lake Chad might have also contributed to control the abundance of these taxa. Changes in the structure and floristic composition of the vegetation towards more open and drier formations occurred after ca. 6050 cal yr BP, following a decrease in mean Pann estimates to approximately 600 ( 230/+600) mm. But, the constant significant presence of lowland humid taxa until ca. 5000 cal yr BP, contemporaneous with a slight increase in steppic taxa, demonstrates that at this date, the modern vegetation was not yet established in the vicinity of Lake Chad. Our data indicate that between ca. 6700 and ca. 5000 cal yr BP vegetation and climate changes must have occurred progressively, but that century-scale climate variability was superimposed on this long-term mid-Holocene drying trend as observed around ca. 6300 cal yr BP, where pollen data indicate more humid conditions.