<p>In recent decades, extensive mortality of reef-building corals throughout the Caribbean region has led to erosion of reef frameworks and declines in biodiversity. Using field observations, structural models and high-precision U-th dating methods, we quantify changes in structural complexity in the major framework building coral <i>Orbicella annularis</i> over a 20-year period at Long Cay (Belize). Despite extensive mortality following the mass coral bleaching event of 1998, structural complexity of frameworks remained largely unchanged between 1998 (rugosity index = 2.35 ± 0.1) and 2018 (2.29 ± 0.1). Reef-scale structural complexity was maintained through rapid growth of surviving ramets (0.69 ± 0.1 cm yr<sup>−1</sup>) offsetting slower bioerosion of dead ramets (−0.11 ± 0.16 cm yr<sup>−1</sup>). Despite apparent stability of structural complexity at reef-scales, bioerosion of individual dead ramets over two decades led to declines in microhabitat complexity, with an overall reduction of the depth of microhabitats within frameworks. Altered microhabitat complexity appears to have negative effects for cryptic fauna, with the grazing urchin Echinometra viridis declining from 1.5 ± 0.4 per m<sup>2</sup> in 1998 to 0.02 ± 0.02 per m<sup>2</sup> in 2018. Changes in microhabitat complexity have the potential to alter ecological interactions that can impact recovery dynamics on coral reefs in ways that are undetectable using reef-scale metrics of structural complexity.</p>