There is increasing evidence that some natural disturbances are increasing in frequency and intensity with global change, but the effects of these changes on plant populations is poorly understood. It is estimated that for every 1°C increase in the summer mean minimum temperature, there is a 40% increase in hail damage. Severe hailstorms can cause large impacts on biological communities. In 2008, a strong hailstorm hit the speciose and endemic rupestrian vegetation in Serra do Cipo, Brazil. This event prompted us to record its effects on the narrowly distributed and threatened species Coccoloba cereifera (Polygonaceae). About 33 to 60% of the leaves on the 246 individuals surveyed were lost. The disturbance also influenced some of the physiological traits of C. cereifera, increasing the concentration of photosynthetic pigments (chlorophyll and carotenoid) and polyphenols in the leaves. The most pronounced increase of chlorophyll was in young leaves (ca. 60%). Carotenoid content increased by ca. 50% in all leaf ages, while polyphenols increased tenfold. Contrarily, the endophyte richness decreased drastically after the event (from 104 to 33 species), only 12% of similar species remain. The hail storm strongly influenced all variables evaluated in this study, i.e., structure, physiology, and associated fungi. These results show that hailstorm had a dramatic and immediate impact on C. cereifera and may also severely affect other endemic or threatened plant species. Therefore, it is imperative that we broaden our knowledge on global climate change impacts for the conservation of native species.