Alteration of ecosystem processes by invasive species can lead to the decline of native species. Management actions targeted at removing these invaders and restoring native populations may have knock-on effects on non-target native species and ecosystems. For example, coastal dunes in the Pacific Northwest of North America are nearly monocultures of the introduced beach grasses, Ammophila arenaria and Ammophila breviligulata. These invasive grasses have converted open, low-lying sand dunes with a sparse covering of native plants to tall, densely-vegetated ridges dominated by the two invaders. As a result, the critical open-sand habitat of the federally threatened Western Snowy plover (Charadrius alexandrinus nivosus) has declined along with populations of several native dune plant species. Here we investigate how nearly 20 years of management targeted at the removal of Ammophila for plover recovery are impacting native plant species and dune morphology along 500 km of coastline in Oregon and Washington, USA. Despite increased plovers and decreased Ammophila in treated areas, plover habitat restoration also has had the unintentional effect of reducing the richness and abundance of native dune plants. Additionally, frequent Ammophila removal has prevented the re-establishment of the natural disturbance regime and dune function. Based on these findings, we suggest that the Pacific Northwest coastal dune ecosystem would benefit from a more synthetic community-wide management approach.