Desiccation of the Sahara since the middle Holocene has eradicated all but a few natural archives recording its transition from a “green Sahara” to the present hyperarid desert. Our continuous 6000-year paleoenvironmental reconstruction from northern Chad shows progressive drying of the regional terrestrial ecosystem in response to weakening insolation forcing of the African monsoon and abrupt hydrological change in the local aquatic ecosystem controlled by site-specific thresholds. Strong reductions in tropical trees and then Sahelian grassland cover allowed large-scale dust mobilization from 4300 calendar years before the present (cal yr B.P.). Today’s desert ecosystem and regional wind regime were established around 2700 cal yr B.P. This gradual rather than abrupt termination of the African Humid Period in the eastern Sahara suggests a relatively weak biogeophysical feedback on climate, was relatively weak.