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Characterizing eastern African environmental variability on orbital timescales is crucial to evaluating the hominin evolutionary response to past climate changes. However, there is a dearth of high-resolution, well-dated records of ecosystem dynamics from eastern Africa that cover long time intervals. In the last 1 Myr, there were significant anatomical and cultural developments in Homo, including the origin of Homo sapiens. There were also major changes in global climatic boundary conditions that may have affected eastern African environments, yet potential linkages remain poorly understood. We developed carbon isotopic records from plant waxes (δ13Cwax) and bulk organic matter (δ13COM) from a well-dated sediment core spanning the last ∼1 Myr extracted from the Koora Basin, located south of the Olorgesailie Basin, in the southern Kenya rift. Our record characterizes the climatic and environmental context for evolutionary events and technological advances recorded in the adjacent Olorgesailie Basin, such as the transition from Acheulean to Middle Stone Age tools by 320 ka. A significant shift toward more C4-dominated ecosystems and arid conditions occurred near the end of the mid-Pleistocene Transition, which indicates a link between equatorial eastern African and high-latitude northern hemisphere climate. Environmental variability increases throughout the mid- to late-Pleistocene, superimposed by precession-paced packets of variability modulated by eccentricity. An interval of particularly high-amplitude climate and environmental variability occurred from ∼275 ka to ∼180 ka, synchronous with evidence for the first H. sapiens fossils in eastern Africa. These results support the ‘variability selection hypothesis’ that increased environmental variability selected for adaptable traits, behaviors, and technology in our hominin ancestors.