The removal of invasive species is often one of the first steps in restoring degraded habitats. However, studies evaluating effectiveness of invasive species removal are often limited in spatial and temporal scale, and lack evaluation of both aboveground and belowground effects on diversity and key processes. In this study, we present results of a large 3-year removal effort of the invasive species, Gypsophila paniculata, on sand dunes in northwest Michigan (USA). We measured G. paniculata abundance, plant species richness, plant community diversity, non-native plant cover, abundance of Cirsium pitcheri (a federally threatened species endemic to this habitat), sand movement, arbuscular mycorrhizal spore abundance, and soil nutrients in fifteen 1000 m2 plots yearly from 2007 to 2010 in order to evaluate the effectiveness of manual removal of this species on dune restoration. Gypsophila paniculata cover was greatly reduced by management, but was not entirely eliminated from the area. Removal of G. paniculata shifted plant community composition to more closely resemble target reference plant communities but had no effect on total plant diversity, C. pitcheri abundance, or other non-native plant cover. Soil properties were generally unaffected by G. paniculata invasion or removal. The outlook is good for this restoration, as other non-native species do not appear to be staging a “secondary” invasion of this habitat. However, the successional nature of sand dunes means that they are already highly invasible, stressing the need for regular monitoring to ensure that restoration progresses.