Mid-Pleistocene (1250-450 ka) lipid biomarker accumulation rates and bulk organic geochemical records have been examined from the Angola Basin in the eastern tropical Atlantic to assess the low-latitude environmental changes associated with the onset of the Middle Pleistocene ice ages. In combination with information on lipid sources, we use principal component and spectral analyses to evaluate the main forcing factors of phytoplankton productivity and lipid transport changes. Cross-spectral analyses reveal the phasing in orbitally driven climatic cycles. The average export of marine productivity remained high and unchanged throughout the mid-Pleistocene transition. However, the relative lipid contributions indicate a significant change in the primary-producing ecosystem. Before the growth of mean global ice volume, enhanced siliceous marine production was mainly controlled by monsoonal variations in river runoff, and oceanic upwelling was forced by variations in trade wind zonality. Both precession-driven processes were suppressed by the enlarged global ice mass after the beginning of the mid-Pleistocene transition. With the onset of 100 ka cyclicity, aeolian transport of terrigenous plant waxes and wind-driven coastal and oceanic upwelling strongly increased. From this time onwards, aridification of the continent and strengthening of the trade winds caused profound environmental changes in the tropical realm.