Belowground microbial communities, in both the bulk soil and the rhizosphere surrounding the roots, are known to moderate the outcomes of species interactions in terrestrial plant communities, but this has not been experimentally tested in marine plants. Testing the role of belowground microbial communities in interactions between plant species of different successional stages could provide critical insight into how marine plant communities re-establish after disturbance. Here, we tested if a colonising seagrass species, Halophila ovalis, and mid successional seagrass species, Zostera muelleri, perform differently (i) depending on whether they are planted into unvegetated, their own or the other species’ sediments and (ii) whether they have an intact or disrupted (greatly reduced) rhizosphere bacterial community. We found Z. muelleri and H. ovalis both perform worse in Z. muelleri sediments, reflecting differences in rhizosphere bacterial community composition between sediment types. In addition, Z. muelleri performs worse with an intact compared to a disrupted rhizosphere bacterial community suggesting that Z. muelleri develops negative belowground feedbacks with its own and other species. These findings can help pre-empt negative outcomes in restoration and management contexts to better restore threatened seagrass and other marine plant communities.