AbstractIn the boreal summer of 2021, the equatorial Atlantic experienced the strongest warm event, that is, Atlantic Niño, since the beginning of satellite observations in the 1970s. Such events have far‐reaching impacts on large‐scale wind patterns and rainfall over the surrounding continents. Yet, developing a paradigm of how Atlantic Niño interacts with the upper‐ocean currents and intraseasonal waves remains elusive. Here we show that the equatorial Kelvin wave associated with the onset of the 2021 Atlantic Niño modulated both the background flow and the eddy flux of the equatorial upper‐ocean circulation, causing an extremely weak and delayed tropical instability wave (TIW) season. TIW‐induced variations of sea surface temperature (SST), sea surface salinity, sea surface height, and eddy temperature advection were exceptionally weak during May to July, the climatological peak of TIW activity, but rebounded in August when higher than normal variability was observed. Moored velocity data at 23°W show that during the peak of the 2021 Atlantic Niño from June to August, the Equatorial Undercurrent was deeper and stronger than usual. An anomalously weak eddy momentum flux strongly suppressed barotropic energy conversion north of the equator from May to July, likely contributing to low TIW activity. Reduced baroclinic energy conversion also might have played a role, as the meridional gradient of SST was sharply reduced during the Atlantic Niño. Despite extremely weak TIW velocities, modest intraseasonal variability of chlorophyll‐a (Chl‐a) was observed during the Atlantic Niño, due to pronounced meridional Chl‐a gradients that partly compensated for the weak TIWs.