Globally, fire is a primary agent for modifying environments through the long-term coupling of human and natural systems. In southern Africa, control of fire by humans has been documented since the late Middle Pleistocene, though it is unclear when or if anthropogenic burning led to fundamental shifts in the region's fire regimes. To identify potential periods of broad-scale anthropogenic burning, we analyze aggregated Holocene charcoal sequences across southern Africa, which we compare to paleoclimate records and archaeological data. We show climate-concordant variability in mid-Holocene fire across much of the subcontinent. However, increased regional fire activity during the late Holocene (∼2000 BP) coincides with archaeological change, especially the introduction and intensification of food production across the region. This increase in fire is not readily explained by climate changes, but rather reflects a novel way of using fire as a tool to manage past landscapes, with outcomes conditioned by regional ecosystem characteristics.