Recurrent sea urchin mass mortality has recently affected eastern Atlantic populations of the barren-forming sea urchin Diadema africanum. This new episode of die-off affords the opportunity to determine common meteorological and oceanographic conditions that may promote disease outbreaks. The population dynamics of this sea urchin species are well known—urchin barrens have persisted for many decades along most of the coastlines off the archipelagos of Madeira, Selvages and the Canary Islands, where they limit macroalgae biomass growth. However, this new and explosive mortality event decimated the sea urchin population by 93% on Tenerife and La Palma Islands. Two severe episodes of southwestern rough sea that lead to winter storms, in February 2010 (Xynthia) and February 2018 (Emma), preceded both mass mortality events. The autumn and winter months of those years were anomalous and characterized by swells with an average wave height above 2 m that hit the south and southwest sides of the islands. The amoeba Paramoeba brachiphila was the only pathogen isolated this time from the moribund and dead sea urchins, suggesting that the amoeba was the primary cause of the mortality. This new sea urchin die-off event supports the “killer-storm” hypothesis that has been already described for western Atlantic coasts. These anomalous southwest storms during winters generate pronounced underwater sediment movement and large-scale vertical mixing, detected in local tide gauge, which may promote paramoebiasis. This study presents valuable insights about climate-mediated changes in disease frequency and its impacts on the future of coastal marine ecosystems in the Atlantic.