The initiation of the Benguela upwelling has been dated to the late Miocene, but estimates of its sea surface temperature evolution are not available. This study presents data from Ocean Drilling Program (ODP) Site 1085 recovered from the southern Cape Basin. Samples of the middle Miocene to Pliocene were analyzed for alkenone-based (U37K′, SSTUK) and glycerol dialkyl glycerol tetraether (GDGT) based (TEX86, TempTEX) water temperature proxies. In concordance with global cooling during the Miocene, SSTUK and TempTEX exhibit a decline of about 8°C and 16°C, respectively. The temperature trends suggest an inflow of cold Antarctic waters triggered by Antarctic ice sheet expansion and intensification of Southern Hemisphere southeasterly winds. A temperature offset between both proxies developed with the onset of upwelling, which can be explained by differences in habitat: alkenone-producing phytoplankton live in the euphotic zone and record sea surface temperatures, while GDGT-producing Thaumarchaeota are displaced to colder subsurface waters in upwelling-influenced areas and record subsurface water temperatures. We suggest that variations in subsurface water temperatures were driven by advection of cold Antarctic waters and thermocline adjustments that were due to changes in North Atlantic deep water formation. A decline in surface temperatures, an increased offset between temperature proxies, and an increase in primary productivity suggest the establishment of the Benguela upwelling at 10 Ma. During the Messinian Salinity Crisis, between 7 and 5 Ma, surface and subsurface temperature estimates became similar, likely because of a strong reduction in Atlantic overturning circulation, while high total organic carbon contents suggest a “biogenic bloom.” In the Pliocene the offset between the temperature estimates and the cooling trend was reestablished.