Recurrent climate-driven warming events, which can induce severe coral bleaching and mortality on tropical reefs, are predicted to cause homogenisation of coral communities and loss of ecosystem functions in shallow reef systems (< 30 m). However, data documenting the variation in coral carbonate production across depth are limited. Here we explore differences in coral cover, community composition, coral colony size structure and carbonate production rates between two depths (10 m and 17.5 m) across four atolls in the remote Chagos Archipelago. We show higher coral carbonate production rates at 10 m (4.82 ± 0.27 G, where G = kg CaCO3 m−2 yr−1) compared to sites at 17.5 m (3.1 ± 0.18 G). The main carbonate producers at 10 m consisted of fast-growing branching and tabular corals (mainly Acroporids) and massive corals (mainly Porites), with high abundances of medium- and large-sized colonies. In contrast, coral carbonate production at 17.5 m was driven by slow-growing encrusting and foliose morphotypes and small colony sizes. Utilising a dataset following 6–7 years of recovery after the 2015–2017 bleaching event, our results show that depth-homogenisation of coral communities was temporary and carbonate production rates at 10 m depth recovered quicker at 3 of 4 studied atolls. The exception is Great Chagos Bank where slower recovery of branching and tabular corals at 10 m has led to a longer-lasting depth-homogenisation of carbonate production rates. The latter example cautions that more frequent bleaching events may drive increasing homogenisation of carbonate production rates across depth gradients, with implications for vital reef geo-ecological functions.