The equatorial Pacific and Atlantic oceans exhibit remarkable meridional undulations in temperature and chlorophyll fronts visible from space over thousands of kilometers and often referred to as tropical instability waves. Here, we present new observations of an ecosystem ranging through three trophic levels: phytoplankton, zooplankton and small pelagic fish whirling within a tropical vortex of the Atlantic ocean and associated with such undulations. Cold, nutrient and biologically rich equatorial waters are advected northward and downward to form sharp fronts visible in all tracers and trophic levels. The equatorward recirculation experiences upwelling at depth, with the pycnocline and ecosystem progressively moving toward the surface to reconnect with the equatorial water mass. The observations thus indicate that it is a fully three-dimensional circulation that dominates the distribution of physical and biological tracers in the presence of tropical instabilities and maintains the cusp-like shapes of temperature and chlorophyll observed from space.