ABSTRACT Many reef ecosystems around the world are threatened by invasive alien species. On the Brazilian coast, the invasive bivalve Isognomon bicolor has recently undergone an expansion in distribution and abundance. In this study, we evaluate the impact of invasive I. bicolor on the native benthic community through an in situ experiment in which the invasive species was removed and the benthic community monitored over the following year. Post‐removal, significant changes were observed in the structure of the native community, but the results were different in the two studied sites. We conclude that the establishment of I. bicolor on consolidated substrates can change the structure of the benthic community. Knowledge about the interactions between native and invasive species and how this species alters native communities in different environments is essential for predicting the course of future invasions and mitigating the impacts caused.