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Structural complexity underpins the ecological functioning of coral reefs. However, rising ocean temperatures and associated coral bleaching threaten the structural integrity of these important ecosystems. Despite the increased frequency of coral bleaching events, few studies to date have examined changes in three-dimensional (3D) reef structural complexity following severe bleaching. The influence of local stressors on reef complexity also remains poorly understood. In the wake of the 2015-2016 El Nino-induced mass coral bleaching event, we quantified the effects of severe heat stress on 3D reef structural complexity across a gradient of local human disturbance. Using Structure-from-Motion photogrammetry we created 3D reconstructions of permanent reef plots and observed substantial declines in reef structural complexity, measured as surface rugosity and terrain ruggedness, and a detectable loss of habitat volume one year after the bleaching event. 3D reef complexity also declined with increasing levels of human disturbance, and with decreasing densities of branching and massive corals. These findings improve our understanding of the effects of local and global stressors on the structural foundation of coral reef ecosystems. In the face of accelerating climate change, mitigating local stressors may increase reef structural complexity, thereby heightening reef resilience to future bleaching events.