AbstractThe ecology and structure of many tropical coral reefs have been markedly altered over the past few decades. Although long‐term recovery has been observed in terms of coral cover, it is not clear how novel species configurations shape reef functionality in impaired reefs. The identities and life‐history strategies of the corals species that recover are essential for understanding reef functional dynamics. We used a species identity approach to quantify the physical functionality outcomes over a 13 year period across 56 sites in the Mexican Caribbean. This region was affected by multiple stressors that converged and drastically damaged reefs in the early 2000s. Since then, the reefs have shown evidence of a modest recovery of coral cover. We used Bayesian linear models and annual rates of change to estimate temporal changes in physical functionality and coral cover. Moreover, a functional diversity framework was used to explore changes in coral composition and the traits of those assemblages. Between 2005 and 2018, physical functionality increased at a markedly lower rate compared to that of coral cover. The disparity between recovery rates depended on the identity of the species that increased (mainly non‐framework and foliose‐digitate corals). No changes in species dominance or functional trait composition were observed, whereas non‐framework building corals consistently dominated most reefs. Although the observed recovery of coral cover and functional potential may provide some ecological benefits, the long‐term effects on reef frameworks remain unclear, as changes in the cover of key reef‐building species were not observed. Our findings are likely to be representative of many reefs across the wider Caribbean basin, as declines in coral cover and rapid increases in the relative abundance of weedy corals have been reported regionally. A coral identity approach to assess species turnover is needed to understand and quantify changes in the functionality of coral reefs.