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<p>In recent decades, extensive mortality of reef-building corals throughout the Caribbean region has led to the 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 Caye (Belize). Despite extensive mortality following the mass coral bleaching event of 1998, the structural complexity of frameworks remained largely unchanged between 1998 (rugosity index, <span class="inline-formula"><i>R</i></span>, of <span class="inline-formula">2.35±0.1</span>) and 2018 (<span class="inline-formula"><i>R</i></span> of <span class="inline-formula">2.29±0.1</span>). Colony-scale structural complexity was maintained, as the rapid growth of surviving ramets (<span class="inline-formula">0.69±0.1</span>&thinsp;cm&thinsp;yr<span class="inline-formula">⁻¹</span>) offset the slower bioerosion of dead ramets (<span class="inline-formula"><math xmlns="http://www.w3.org/1998/Math/MathML" id="M7" display="inline" overflow="scroll" dspmath="mathml"><mrow><mo>-</mo><mn mathvariant="normal">0.11</mn><mo>±</mo><mn mathvariant="normal">0.16</mn></mrow></math><span><svg:svg xmlns:svg="http://www.w3.org/2000/svg" width="64pt" height="10pt" class="svg-formula" dspmath="mathimg" md5hash="2b45054c9badb1949fab9d9db4d58638"><svg:image xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="bg-17-5909-2020-ie00001.svg" width="64pt" height="10pt" src="bg-17-5909-2020-ie00001.png"/></svg:svg></span></span>&thinsp;cm&thinsp;yr<span class="inline-formula">⁻¹</span>). Despite the apparent stability of the structural complexity at colony scales, bioerosion of individual dead ramets over 2 decades led to declines in microhabitat complexity, with an overall reduction in the depth of microhabitats within frameworks. Altered microhabitat complexity appears to have negative effects on cryptic fauna, with the grazing urchin <i>Echinometra viridis</i> declining from <span class="inline-formula">1.5±0.4</span>&thinsp;individuals&thinsp;m<span class="inline-formula">⁻²</span> in 1998 to <span class="inline-formula">0.02±</span>&thinsp;individuals&thinsp;m<span class="inline-formula">⁻²</span> 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 traditional rugosity metrics of structural complexity.</p>