Coral-associated microbial communities are essential for the health of the host and could mediate its adaptation in the face of climate change. Microbiome manipulation provides promising potential in enhancing coral performance and could be implemented in coral nurseries to promote juvenile survival in reef restoration initiatives. In this study, we reared early Pocillopora acuta recruits either in filtered seawater, or in the vicinity of P. acuta or P. daedalea adult fragments to investigate whether the presence of different adult corals could influence the recruit microbiome. Following four weeks of exposure, recruits were transferred to a mesocosm to simulate transplant to the field. As recruit-associated ^ bacterial assemblages did not differ across treatments, we conclude that using a flow-through system is not an effective inoculation strategy. The temporal dynamics of bacterial assemblages in coral recruits also highlight the need of stronger inoculations to ensure that stable associations are established.