Environmental shifts can cause epigenetic modifications in corals, which are associated with changes in gene expression and physiology, though it remains unclear if associated bacteria can also induce such changes. Here, we inoculate nubbins of the coral Pocillopora verrucosa with an opportunistic pathogen, Vibrio coralliilyticus, and/or a coral probiotic, Cobetia sp., and subject the nubbins to heat stress. We show that pathogen exposure leads to distinct DNA methylation changes compared to the control, probiotic, and co-inoculation groups. We also confirm that DNA methylation broadly correlates with coral gene expression; however, individual correlations are restricted to a subset of genes. We then highlight genes altered by pathogen inoculation that show similar responses in their expression and methylation. Notably, coral probiotic exposure mitigates specific epigenetic changes caused by pathogen inoculation, which correlates with increased stress resilience and higher coral survival rates. Although many aspects remain to be resolved, evidence that bacteria alter coral epigenomes may help clarify the role of microbiome interactions in coral resilience.