Efforts to manage coral reef declines are increasingly turning towards in situ propagation of corals to aid reef recovery. Yet the extent to which propagation practices potentially impact the underlying coral biology, and subsequent restoration ‘success’, remains unknown. Given the importance of the coral microbiome, we examined the influence of propagation and out-planting, over four months and one month respectively, on the microbiome of two coral species Acropora millepora and Pocillopora verrucosa. Coral host species-specific temporal dynamics were observed during the transplantation of corals into nurseries and subsequent out-planting back to the reef. P. verrucosa bacterial communities remained stable throughout propagation, out-planting and within the natural reef environment. In contrast, A. millepora bacterial communities exhibited changes within coral nurseries and after out-planting that were not seen in the source colonies. We interpret the shifts of A. millepora bacterial communities within the nursery as an impact of distinctive environmental conditions in nurseries compared to natural reef settings, and the greater responsiveness of A. millepora microbiome to environmental change. Our observations highlight that different coral species exhibit distinct microbial responses to propagation and out-planting, and we recommend that these should be considered when designing and scaling future reef management strategies.