The resilience of reefs to repeated, increasingly frequent thermal disturbance is a dynamic balance between resistance and recovery pathways. The Lakshadweep archipelago in the central Indian Ocean has experienced three El Nin˜o Southern Oscillation (ENSO) events in 1998, 2010 and 2016. Using a multi-decadal monitoring of 6 shallow reefs, we estimated reef resistance and coral recovery after each of these bleaching events. Even as the severity of each ENSO event increased over time, coral mortality decreased from 87% post-1998 to 44% after 2010 and 31% after 2016. In contrast, benthic recovery after 2010 was more protracted than after 1998, with a fourfold decrease in recovery rates between the two time periods. This has resulted in a 40% decline in absolute coral cover in the last 2 decades from 51.6% in 1998 to 11% in 2017. We examined the demographic and compositional mechanisms underlying these two recovery trajectories by monitoring coral recruitment, juvenile, and young adult compositions for 5 yr after 1998 and 2010. While coral juvenile densities were comparable after each of these disturbances, densities of fast-growing Acroporids had reduced from[1 m-2 post-1998 to 0.09 m-2 post-2010. This was reflected in the composition of coral communities in 2003 and 2015, which differed in its dominant coral taxa, with a dramatic decline in Acropora and an increase in the cover of Porites by 2015. While the dominance of resistant taxa like Porites signals a shift to a system adapting to recurrent thermal anomalies, the reduction in fast-growing, habitat-forming corals like Acropora is driving a major decline in recovery rates with time. Given the frequency of current warming events, the increased reef resistance over the last 2 decades is likely not sufficient to also ensure gains in coral cover in Lakshadweep’s reefs.