Isolated coral reef habitats are unique systems to study the natural dynamics of coral traits and their natural acclimatization, adaptation, and recovery from global-scale stressors such as thermally induced bleaching events. This study evaluates the spatial and temporal changes in coral community attributes (diversity, live cover, and coral assemblage structure) over 14 years (2005–2019) at Clipperton, an extremely remote Eastern Tropical Pacific (ETP) atoll. The atoll exhibited overall high coral cover (~ 50–60%) dominated by massive species (Porites spp.), yet we observed large variation (44–56%) in coral community attributes among survey years (2005, 2016, 2019) with depth explaining most of the variation. Live coral cover increased in 2019 after a severe thermal stress event (El Niño, 2015–2016) and many tropical cyclones, which also caused a shift in assemblage structure from branching Pocillopora to massive Porites in the shallower reef zones, resulting in a less well-defined depth gradient. These changes in coral assemblage structure may have long-term effects on the configuration of the physical reef framework of the well-conserved coral reef ecosystems at Clipperton and consequently may alter the ecological functionality of one of the most important biogeographic stepping stones in the central Pacific and ETP regions.