Anthropogenic climate change is intensifying natural disturbance regimes, which negatively affects some species, while benefiting others. This could alter the trait composition of ecological communities and influence resilience to disturbance. We investigated how the frequency and intensification of the regional storm regime (and likely other disturbances) is altering coral species composition and in turn resistance and recovery. We developed regional databases of coral cover and composition (3144 reef locations from 1970 to 2017) and of the path and strength of cyclonic storms in the region (including 10,058 unique storm-reef intersections). We found that total living coral cover declined steadily through 2017 (the median annual loss rate was ~ 0.25% per year). Our results also indicate that despite the observed increase in the intensity of Atlantic cyclonic storms, their effect on coral cover has decreased markedly. This could be due in part to selection for disturbance-resistant taxa in response to the intensifying disturbance regime. We found that storms accelerated the loss of threatened acroporid corals but had no measurable effect on the cover of more resilient “weedy” corals, thereby increasing their relative cover. Although resistance to disturbance has increased, recovery rates have slowed due to the dominance of small, slow-growing species. This feedback loop is locking coral communities into a low-functioning state dominated by weedy species with limited ecological or societal value.