During the Late Miocene, Africa experienced a number of ecological transitions including the spread of C4 grasslands, the expansion of the Sahara Desert, the Messinian Salinity Crisis and a number of mammalian migrations and expansions, including the origin of the hominin clade. A detailed understanding of the relationship between environmental change and hominin evolution is hampered by the paucity of data available from terrestrial localities, especially in southern Africa. Here, we present a stable isotope and trace element record from a speleothem from the South African cave site of Hoogland. Uranium-lead dating and magnetostratigraphy places the speleothem within the Messinian Age (7.25–5.33 Ma) of the Late Miocene, making it the oldest known cave deposit from the region near the UNESCO Fossil Hominids of South Africa World Heritage Site (locally known as the “Cradle of Humankind”). Low carbon isotope values indicate a predominantly C3 vegetation in the vicinity of the cave throughout the period of speleothem growth. It is not possible to determine if this represents a C3 grassland or a C3 woodland, but it is clear that an equivalent C3-rich environment has yet to be found during the Messinian of east Africa. We conclude that the C4 grass expansion occurred millions of years later in South Africa than it did in eastern Africa, and that this vegetation shift should be considered when comparing African vegetation change with the late Miocene hominin fossil record.