El Niño, the most prominent climate fluctuation at seasonal-to-interannual timescales, has long been known to have a remote impact on climate variability in the tropical Atlantic Ocean, but a robust influence is found only in the northern tropical Atlantic region. Fluctuations in the equatorial Atlantic are dominated by the Atlantic Niño, a phenomenon analogous to El Niño, characterized by irregular episodes of anomalous warming during the boreal summer. The Atlantic Niño strongly affects seasonal climate prediction in African countries bordering the Gulf of Guinea. The relationship between El Niño and the Atlantic Niño is ambiguous and inconsistent. Here we combine observational and modelling analysis to show that the fragile relationship is a result of destructive interference between atmospheric and oceanic processes in response to El Niño. The net effect of El Niño on the Atlantic Niño depends not only on the atmospheric response that propagates the El Niño signal to the tropical Atlantic, but also on a dynamic ocean-atmosphere interaction in the equatorial Atlantic that works against the atmospheric response. These results emphasize the importance of having an improved ocean-observing system in the tropical Atlantic, because our ability to predict the Atlantic Niño will depend not only on our knowledge of conditions in the tropical Pacific, but also on an accurate estimate of the state of the upper ocean in the equatorial Atlantic.