Overfishing major predators has dramatically changed the trophic structures of coral reefs. Here, we argue that the photosynthate, which would normally support the large predators via trophic transfers, is being used by microbes (Bacteria and Archaea) on degraded reefs. The supply of higher concentrations of photosynthate to the microbes increases their population size and enables heterotrophic microbes to dominate the community. In turn, the heterotrophic microbes detrimentally affect the corals causing disease outbreaks and death, which causes the phase shift from coral to fleshy algae (including macroalgae and turf algae) dominated reefs. To succeed, conservation and restoration efforts need to understand and consider the influence of microbes.