The variability of sea surface temperature (SST) in the equatorial Atlantic is characterized by strong cooling in May–June and a secondary cooling in November–December. A numerical simulation of the tropical Atlantic is used to diagnose the different contributions to the temperature tendencies in the upper ocean. Right at the equator, the coolest temperatures are observed between 20°W and 10°W due to enhanced turbulent heat flux in the center of the basin. This results from a strong vertical shear at the upper bound of the Equatorial Undercurrent (EUC). Cooling through vertical mixing exhibits a semiannual cycle with two peaks of comparable intensity. During the first peak, in May–June, vertical mixing drives the SST while during the second peak, in November–December, the strong heating due to air-sea fluxes leads to much weaker effective cooling than during boreal summer. Seasonal cooling events are closely linked to the enhancement of the vertical shear just above the core of the EUC, which appears to be not driven directly by the strength of the EUC but by the strength and the direction of the surface current. The vertical shear is maximum when the northern branch of the South Equatorial Current is intense. The surface cooling in the eastern equatorial Atlantic is not as marked as in the center of the basin. Mean thermocline and EUC rise eastward, but a strong stratification, caused by the presence of warm and low-saline surface waters, limits the vertical mixing to the upper 20 m and disconnects the surface from subsurface dynamics.