El Niño is generally associated with below-average rainfall in northeastern Brazil (NEB). In 2019, however, the opposite rainfall pattern was observed during an El Niño episode. Here, we explore the mechanisms that overwhelmed typical El Niño-related conditions and resulted in above-average rainfall in NEB. We focus on the austral autumn, when El Niño is most related to rainfall anomalies in the region. The analysis of rainfall data from weather stations and the Global Precipitation Climatology Project, upper- and lower-level circulation reanalysis data, sea surface temperature data, outgoing longwave radiation data, and modelled data allowed us to identify that the autumn 2019 heavy rainfall in NEB was likely associated with three combined factors; these are: (1) the weak intensity of the 2019 El Niño; (2) local and remote diabatic heating anomalies, especially over the western South Pacific and tropical South Atlantic, which resulted in anticyclonic and cyclonic circulations in the upper and lower troposphere, respectively, over the tropical South Atlantic; and (3) sub-seasonal atmospheric convection anomalies over the western South Pacific, which reinforced the low-frequency convection signal over that region. This latter factor suggests the influence of the Madden–Julian Oscillation on rainfall in NEB during the first ten days of March. We discuss these mechanisms in detail and provide evidence for their associations with the anomalously heavy rainfall in NEB. Our results may assist in the planning of several crucial activities, such as water resources management and agriculture.