Mass bleaching events are growing in duration and intensity. Besides causing extensive mortality, the progressively shorter time between events disrupts the ability of reefs to recover. The unique reefs of the Southwestern Atlantic are often considered climate refugia as they have suffered less bleaching-related mortality when compared to Indo–Pacific and Caribbean reefs. However, their recovery capacity still requires investigation. In 2019, an unprecedented heatwave triggered the most severe bleaching episode recorded for Southwestern Atlantic reefs. Therefore, this study aimed to (i) document the bleaching incidence and mortality during the heatwave, and (ii) assess coral recovery over 3 years. We measured bleaching incidence and monitored coral cover through surveys in three Southern Bahia (central Brazilian coast) reefs before, during and after thermal stress. Our findings show that coral assemblages were exposed to a 5-month-long thermal anomaly, experiencing thermal stress peaking at 14.1 ºC-weeks. Roughly 70% of the coral cover was bleached, resulting in a decline of ~ 40%. Millepora alcicornis, Mussismilia braziliensis, and Mussismilia harttii were among species that mortality exceeded 50%. After 3 years, corals showed no increase in cover neither at assemblage nor species levels. This constrained recovery capacity may indicate the breakdown of the refugium, and also trade-off for resistance. Typical features of the region, such as high turbidity and the dominance of massive corals, provide these reefs with bleaching resistance, but likely also limit their recovery. With the anticipated effects of the 2023–24 El Niño–Southern Oscillation in the southern hemisphere, still unrecovered Southwestern Atlantic reefs face a substantial challenge.