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The drivers of the evolution of the South Asian Monsoon remain widely debated. An intensification of monsoonal rainfall recorded in terrestrial and marine sediment archives from the earliest Miocene (23-20 million years ago (Ma)) is generally attributed to Himalayan uplift. However, Indian Ocean palaeorecords place the onset of a strong monsoon around 13 Ma, linked to strengthening of the southwesterly winds of the Somali Jet that also force Arabian Sea upwelling. Here we reconcile these divergent records using Earth system model simulations to evaluate the interactions between palaeogeography and ocean-atmosphere dynamics. We show that factors forcing the South Asian Monsoon circulation versus rainfall are decoupled and diachronous. Himalayan and Tibetan Plateau topography predominantly controlled early Miocene rainfall patterns, with limited impact on ocean-atmosphere circulation. The uplift of the East African and Middle Eastern topography played a pivotal role in the establishment of the modern Somali Jet structure above the western Indian Ocean, while strong upwelling initiated as a direct consequence of the emergence of the Arabian Peninsula and the onset of modern-like atmospheric circulation. Our results emphasize that although elevated rainfall seasonality was probably a persistent feature since the India-Asia collision in the Paleogene, modern-like monsoonal atmospheric circulation only emerged in the late Neogene.