© 2020, Senckenberg Gesellschaft für Naturforschung. Ecosystem engineer species create enhanced habitat resources, and therefore host exceptionally diverse communities. We studied the case of two ecosystem engineers: a non-native ascidian, Pyura praeputialis, and the native mussel, Perumytilus purpuratus, in the rocky shores of Antofagasta Bay, northern Chile. P. praeputialis was once dominant in mid- and low-intertidal zones, but human harvesting has severely reduced the extent of the P. praeputialis band, allowing for competition from P. purpuratus, which subsequently expanded and replaced P. praeputialis. We compared the macrobenthic community structure between these two ecosystem engineers at five sites throughout the bay. Our results suggest not only an important share of species composition between the ecosystem engineers (68.1%) but also dissimilarity due to differential changes in taxa abundance. Taxonomic richness and diversity were always high in both ecosystem engineers when analyzing communities in areas without these engineers. Diversity recorded in P. praeputialis was slightly higher than those in P. purpuratus; however, the re-establishment of the native mussel could prevent a substantial drop in diversity as the invasive bioengineer disappears. From a biogeographical standpoint, all recorded taxa associated with both ecosystem engineers were native, thus allowing us to conclude that P. praeputialis did not further facilitate the presence of invasive species; rather, this bioengineer could be considered a reservoir of native fauna. Our study highlights the importance of the coexistence of multiple ecosystems engineers and their interactions in the maintenance of biodiversity in rocky shores, especially in cases where human disturbance reduces the more dominant but invasive ecosystem engineer.