Studying monsoon dynamics during past warm time periods such as the Miocene Climatic Optimum (MCO; ∼16.9–14.5 Ma) could greatly aid in better projecting monsoon intensity, in the context of future greenhouse warming. However, studies on regional MCO temperature change and its effect on the monsoons during this time period are lacking. Here, we present the first high‐resolution, low‐latitude record of sea surface temperature (SST) and paleoceanographic change covering the Miocene Climatic Optimum, in the eastern equatorial Atlantic, at Ocean Drilling Program Site 959, based on TEX86 paleothermometry. SSTs were ∼1.5°C warmer at the onset of the MCO (16.9 Ma) relative to the pre‐MCO (∼18.3–17.7 Ma). This warming was accompanied by a transient increase in %total organic carbon. Prior to the MCO, sediment composition, geochemical proxy data as well as dinoflagellate cyst assemblages imply a productive surface ocean at Site 959. Immediately following the MCO onset (∼16.9–16.5 Ma), we record an intensification of the West African Monsoon (WAM) characterized by higher amplitude variability in all proxy records on precession to obliquity timescales. We interpret increased orbital‐scale SST, biogenic Ba and dinocyst assemblage variability to represent intensification of equatorial upwelling, forced by the WAM strength. Furthermore, higher SSTs during eccentricity maxima correlate to increased relative abundances of the warm and stratification‐favoring dinocyst Polysphaeridium zoharyi, during periods of low WAM intensity. Finally, while long‐term SSTs decline toward the middle Miocene, maximum SSTs and Polysphaeridium zoharyi abundances occur during MCO peak warming at ∼15.6 Ma.