Reef habitats, both natural and humanmade, play a vital role in marine ecosystems by providing structure, shelter and resources for a range of different species. New anthropogenic marine structures function as new substrate and can be seen as an artificial reef. Implementing nature-based solutions enhances the ecological value of the structure and this approach is increasingly adopted. Artificial reefs are widely studied, yet predicting their community composition compared to natural reefs remains challenging. This case-study assesses how comparable the community compositions, including number and type of non-indigenous species (NIS), on an artificial and natural oyster reef are after 13 years of succession. Additionally, we examine the impact of morphology- and genomics-based identification methods on alpha and beta diversity using eDNA metabarcoding of water samples and morphological identifications of hand-collected animals from tidal pools collected at three timepoints. Finally, we compared the species and biological traits detected by the two methods. Both reefs showed similar community composition and prevalence of NIS. The artificial reef did not appear to facilitate the spread of NIS more than the natural reef at this stage of development. In addition, eDNA outperformed hand-collection in the detection of highly mobile, sessile and filter feeding species, while hand-collection of animals better identified burrowing and tube-dwelling organisms. We conclude that the artificial reef closely resembled the natural one, demonstrating successful ecological integration. These findings can inform nature-based construction and emphasize the need for tailored long-term monitoring based on target taxa and associated traits.