The resistance of corals to a changing climate has been linked to physiological parameters including heterotrophic capacity and energy reserves. Recently, the potential flexibility and diversity of coral-associated microbial communities have also been related to coral health and resistance to environmental stress. This study uses the island of O‘ahu in Hawai‘i, USA, as a natural laboratory to explore variability in the microbial community composition of four coral species (Porites compressa, Porites lobata, Pocillopora acuta, and Pocillopora meandrina) across a gradient of natural ocean conditions. In addition, we assessed potential relationships between the composition of coral-associated microbial communities with coral physiology. We found that microbial community composition differed among all coral species, as well as among several of the collection sites within species. Microbial community assembly appeared to be governed by a combination of deterministic and stochastic processes, and the composition of these communities was more often related to measurements of coral physiology than environmental parameters among the collection sites. Specifically, coral lipid and protein levels, two components of coral energy reserves, explained significant portions of microbial community composition in Porites lobata and Pocillopora acuta, respectively. Further, microbial community diversity decreased as the proportionate contribution of heterotrophy relative to photoautotrophy in coral tissues increased in Porites compressa and Pocillopora acuta, but the opposite was true for Porites lobata. These findings suggest that if coral heterotrophy increases with warming oceans, it could co-occur with shifts in microbial community diversity in some coral species, possibly from decreased production of photosynthates and/or changes in the nutritional makeup of the mucus layer. Overall, connections with energy reserves and heterotrophy suggest a role for coral resource use in shaping the composition of coral-associated microbial communities across a range of natural ocean conditions, a relationship that may be important as some corals acclimatize to global climate change.