Microbial communities play an important role in plant ecosystem functioning. In marine systems, below-ground microbes contribute to sediment structure and stabilization, nutrient cycling, and the establishment of plants and associated biodiversity. The decline of marine plants such as seagrasses has prompted the need for restoration, which in many locations is achieved through transplantation of shoots. Most plant restoration efforts assume that once plant species are transplanted and survive, this will lead to changes in below-ground microbes, which will, in turn, influence biodiversity and ecosystem functioning. However, this assumption has not been well established in marine systems. In this study, we investigated the effect of restoring the endangered seagrass species Posidonia australis on sediment microbial communities. We compared sediment bacterial communities, characterized through 16S rRNA gene amplicon sequencing, using two restoration techniques: translocating shoots from nearby meadows and utilizing naturally detached beach-cast fragments. Bacterial communities from restored sites were further compared with sediments collected from reference (extant Posidonia) and control (no restoration) sites eight months after seagrass shoot transplantation. The importance of sediment microbial changes following seagrass restoration and their implications for future restoration efforts will be discussed.