The world’s coral reefs are threatened by the cumulative impacts of global climate change and local stressors. Driven largely by a desire to understand the interactions between corals and their symbiotic microorganisms, and to use this knowledge to eventually improve coral health, interest in coral microbiology and the coral microbiome has increased in recent years. In this review, we summarize the role of the coral microbiome in maintaining a healthy metaorganism by providing nutrients, support for growth and development, protection against pathogens, and mitigation of environmental stressors. We explore the concept of coral microbiome engineering, that is, precise and controlled manipulation of the coral microbiome to aid and enhance coral resilience and tolerance in the changing oceans. Although coral microbiome engineering is clearly in its infancy, several recent breakthroughs indicate that such engineering is an effective tool for restoration and preservation of these valuable ecosystems. To assist with identifying future research targets, we have reviewed the common principles of microbiome engineering and its applications in improving human health and agricultural productivity, drawing parallels to where coral microbiome engineering can advance in the not-too-distant future. Finally, we end by discussing the challenges faced by researchers and practitioners in the application of microbiome engineering in coral reefs and provide recommendations for future work.