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Abstract Based on velocity data from a long‐term moored observatory located at 0°N, 23°W we present evidence of a vertical asymmetry during the intraseasonal maxima of northward and southward upper‐ocean flow in the equatorial Atlantic Ocean. Periods of northward flow are characterized by a meridional velocity maximum close to the surface, while southward phases show a subsurface velocity maximum at about 40 m. We show that the observed asymmetry is caused by the local winds. Southerly wind stress at the equator drives northward flow near the surface and southward flow below that is superimposed on the Tropical Instability Wave (TIW) velocity field. This wind‐driven overturning cell, known as the Equatorial Roll, shows a distinct seasonal cycle linked to the seasonality of the meridional component of the south‐easterly trade winds. The superposition of vertical shear of the Equatorial Roll and TIWs causes asymmetric mixing during northward and southward TIW phases.