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Advances in bioengineering and nanotechnology are revolutionizing how we approach problems deemed unsolvable only a decade ago. Nanotechnology has transformed biomedicine, agriculture, and energy science, with broad translational capacity to natural systems. Coral reef ecosystems provide immense biodiversity and economic value but are being degraded at an unprecedented rate, triggering calls for human interventions such as those that have been applied to biomedical systems. Here, we propose that next-generation nanobiotechnology (nanocarriers, nanobiosensors, 3D bioprinting) can be leveraged to provide solutions for the persistence of future reefs. We advocate initiating critical dialogues and developing translational tools to apply to coral reef ecosystems. We challenge and invite the scientific community and industry to harness and expand the available bioengineering and nanotechnology toolkits for applied monitoring, rehabilitation, restoration, and conservation of coral reefs worldwide.