The Sahara is the largest hot desert on Earth. Yet the timing of its inception and its response to climatic forcing is debated, leading to uncertainty over the causes and consequences of regional aridity. Here we present detailed records of terrestrial inputs from Africa to North Atlantic deep-sea sediments, documenting a long and sustained history of astronomically paced oscillations between a humid and arid Sahara from over 11 million years ago. We show that intervals of strong dust emissions from the heart of the continent predate both the intensification of Northern Hemisphere glaciation and the oldest land-based evidence for a Saharan desert by millions of years. We find no simple long-term gradational transition towards an increasingly arid climate state in northern Africa, suggesting that aridity was not the primary driver of gradual Neogene expansion of African savannah C4 grasslands. Instead, insolation-driven wet–dry shifts in Saharan climate were common over the past 11 Myr, and we identify three distinct stages in the sensitivity of this relationship. Our data provide context for evolutionary outcomes on Africa; for example, we find that astronomically paced arid intervals predate the oldest fossil evidence of hominid bipedalism by at least 4 Myr.