While the diversity of coral microbiomes has been studied extensively, knowledge about their structure and ecological role within the holobiont remains scant. Bacteria from the genus Endozoicomonas are well-known coral symbionts commonly found in cell-associated microbial aggregates (CAMAs) in a wide range of coral species, however, their spatial distribution and function within the coral holobiont remain largely underexplored. In this study, CAMAs from the common reef-building coral Acropora loripes were characterized to provide novel insight into their distribution and functional potential. Twelve distinct coral genotypes were obtained from two separate reef sites in the central Great Barrier Reef and 16S rRNA gene metabarcoding demonstrated that all genotypes harboured Endozoicomonas as their dominant bacterial symbiont. A combination of RNA-targeting hybridization chain reaction fluorescence in situ hybridization (HCR-FISH) and whole-mount observation of corals revealed bacterial clusters to be comprised of Endozoicomonas according to taxon-specific probes. While no significant differences were observed in the occurrence or morphology of CAMAs between reef sites or genotypes, CAMAs were more prevalent in tissue structures found in the upper and lower gastric cavity. The ten most prevalent Endozoicomonas strains revealed by 16S rRNA gene metabarcoding were obtained in pure culture, and their determined high-quality genomes are currently being assembled. This will allow us to investigate their functional potential and develop strain-specific FISH probes to explore whether multiple Endozoicomonas phylotypes coexist inside a single CAMA. This work contributes to the understanding of how tissue-associated bacterial communities influence coral holobiont functioning.