Observations of Jupiter’s deep atmosphere by the Juno spacecraft have revealed several puzzling facts: The concentration of ammonia is variable down to pressures of tens of bars, and is strongly dependent on latitude. While most latitudes exhibit a low abundance, the Equatorial Zone of Jupiter has an abundance of ammonia that is high and nearly uniform with depth. In parallel, the Equatorial Zone is peculiar for its absence of lightning, which is otherwise prevalent most everywhere else on the planet. We show that a model accounting for the presence of small-scale convection and water storms originating in Jupiter’s deep atmosphere accounts for the observations. Where strong thunderstorms are observed on the planet, we estimate that the formation of ammonia-rich hail (’mushballs’) and subsequent downdrafts can deplete efficiency the upper atmosphere of its ammonia and transport it efficiently to the deeper levels. In the Equatorial Zone, the absence of thunderstorms shows that this process is not occurring, implying that small-scale convection can maintain a near-homogeneity of this region. A simple model satisfying mass and energy balance accounts for the main features of Juno’s MWR observations and successfully reproduces the inverse correlation seen between ammonia abundance and the lightning rate as function of latitude. We predict that in regions where ammonia is depleted, water should also be depleted to great depths. This new vision of the mechanisms at play, which are both deep and latitude-dependent, has consequences for our understanding of Jupiter’s deep interior and of giant-planet atmospheres in general.