Savanna ecosystems were the landscapes for human evolution and are vital to modern Sub-Saharan African food security, yet the fundamental drivers of climate and ecology in these ecosystems remain unclear. Here we generate plant-wax isotope and dust flux records to explore the mechanistic drivers of the Northwest African monsoon, and to assess ecosystem responses to changes in monsoon rainfall and atmospheric pCO2. We show that monsoon rainfall is controlled by low-latitude insolation gradients and that while increases in precipitation are associated with expansion of grasslands into desert landscapes, changes in pCO2 predominantly drive the C3/C4 composition of savanna ecosystems.