The Kalahari Basin in southern Africa, shaped by subsidence and epeirogeny, features the Okavango Rift Zone (ORZ) as a significant structural element characterized by diffused extensional deformation forming a prominent depocenter. This study elucidates the Pleistocene landscape evolution of the ORZ by examining the chronology of sediment formation and filling this incipient rift and its surroundings. Modeling of cosmogenic nuclide concentrations in surficial eolian sand from distinct structural blocks around the ORZ provides insights into sand’s residence time on the surface. Sand formation occurred from ~2.2 to 1.1 Ma, coinciding with regional tectonic events. Notably, provenance analyses of sand within ORZ’s lowermost block where large alluvial fans are found indicate different source rocks and depositional environments than those of the more elevated eolian sand. This suggests that the major phase of rift subsidence and the following incision of alluvial systems into the rift occurred after eolian dune formation. Luminescence dating reveals that deposition in alluvial fan settings in the incised landscape began not later than ~250 ka, and that a lacustrine environment existed since at least ~140 ka. The established chronological framework constrains the geomorphological effects of the different tectono-climatic forces that shaped this nascent rifting area. It highlights two pronounced stages of landscape development, with the most recent major deformation event in the evolving rift probably occurring during the middle Pleistocene transition (1.2-0.75 Ma). This event is reflected as a striking change in the depositional environments due to the configurational changes accompanying rift progression.