Southern Africa's unique global position has given rise to a dynamic climate influenced by large sea surface temperature gradients and seasonal fluctuations in the Inter Tropical Convergence Zone. Due to the semi-arid climate of the region, terrestrial palaeorecords are rare and our understanding of the long-term sensitivity of Southern African terrestrial ecosystems to climatic drivers is ambiguous. A 810 cm continuous peat core was extracted from the Mfabeni peatland with a ¹⁴C basal age of c. 47 thousand years calibrated before present (kcal yr BP), positioning it as one of the oldest known sub-tropical coastal peatlands in Southern Africa. This peat core provides an opportunity to investigate palaeoenvironmental changes in subtropical Southern Africa since the late Pleistocene. Biomarker (n-alkane, n-alkanoic acid and n-alkanol) analysis, in conjunction with previously published bulk geochemical data, was employed to reconstruct organic matter (OM) sources, rates of OM remineralisation and peatland hydrology. Our results showed that the principal OM source into the peatland was emergent and terrestrial plants with exception of shallow lake conditions when submerged macrophytes dominated (c. 44.5–42.6, 29.7, 26.1–23.1, 16.7–7.1 and 2.2 kcal yr BP). n-Alkane proxies suggest that local plant assemblages were predominantly influenced by peatland hydrology. By incorporating temperature sensitive n-alkanoic acid and n-alkanol proxies, it was possible to disentangle the local temperature and precipitation changes. We report large variations in precipitation intensities, but subdued temperature fluctuations during the late Pleistocene. The Holocene period was characterised by overall elevated temperatures and precipitation compared to the preceding glacial period, interspersed with a millennial scale cooling event. A close link between the Mfabeni archive and adjacent Indian Ocean marine core records was observed, suggesting the regional ocean surface temperatures to be the dominant climate driver in this region since the late Pleistocene.