A feature of Pliocene climate is the occurrence of “permanent El Niño-like” or “El Padre” conditions in the Pacific Ocean. From the analysis of sediment cores in the modern northern Benguela upwelling, we show that the mean oceanographic state off Southwest Africa during the warm Pliocene epoch was also analogous to that of a persistent Benguela “El Niño”. At present these events occur when massive southward flows of warm and nutrient-poor waters extend along the coasts of Angola and Namibia, with dramatic effects on regional marine ecosystems and rainfall. We propose that the persistent warmth across the Pliocene in the Benguela upwelling ended synchronously with the narrowing of the Indonesian seaway, and the early intensification of the Northern Hemisphere Glaciations around 3.0–3.5 Ma. The emergence of obliquity-related cycles in the Benguela sea surface temperatures (SST) after 3 Ma highlights the development of strengthened links to high latitude orbital forcing. The subsequent evolution of the Benguela upwelling system was characterized by the progressive intensification of the meridional SST gradients, and the emergence of the 100 ky cycle, until the modern mean conditions were set at the end of the Mid Pleistocene transition, around 0.6 Ma. These findings support the notion that the interplay of changes in the depth of the global thermocline, atmospheric circulation and tectonics preconditioned the climate system for the end of the warm Pliocene epoch and the subsequent intensification of the ice ages.