Estimating the mixed‐layer heat budget is a key issue for understanding the cold tongue development in the eastern equatorial Atlantic. A high‐resolution ocean regional model is used to diagnose the mixed‐layer heat budget online during the EGEE‐3 experiment from May to August 2006. The heat budget shows the major role of the horizontal advection and turbulent mixing in the mixed‐layer temperature balance in the cold tongue. The surface net heat flux and entrainment processes play a minor role. The equatorial cooling is mainly induced by low‐frequency advection, which is balanced by high‐frequency zonal and meridional advections. The high‐frequency advections are organized in patterns along the northern edge of the cold tongue, where they are associated with strong sea surface temperature gradients and well‐developed tropical instability waves in the western Atlantic. Special attention is paid to the wind energy flux, which controls horizontal advection and turbulent mixing. We suggest that the wind energy flux drives the vertical velocity, which in turn adjusts the mixed‐layer depth, its stratification, and the vertical shear of the horizontal current. Although vertical advection is not essential in providing cold water in the Atlantic cold tongue, it is shown that the vertical velocity plays a central role in preconditioning the mixed layer and maximizes the turbulent mixing. Key Points Horizontal advection and turbulent mixing drive the cold tongue development Low/high‐frequency advection cools/warms the Equatorial Atlantic Surface wind‐energy flux controls the equatorial mixed‐layer dynamics