Phragmites australis (common reed) has expanded in many wetland habitats. Its ability to exclude other plant species has led to both control and eradication programs. This study examined two control methods—herbicide application or a herbicide-burning combination—for their efficacy and ability to restore plant biodiversity in non-tidal wetlands. Two Phragmites-dominated sites received the herbicide glyphosate. One of these sites was burned following herbicide application. Plant and soil macroinvertebrate abundance and diversity were evaluated pre-treatment and every year for four years post-treatment using belt transects. The growth of Phragmites propagules—seeds, rhizomes, and rooted shoots—was examined in the greenhouse and under bare, burned, or vegetated soil conditions. Both control programs greatly reduced Phragmites abundance and increased plant biodiversity. Plant re-growth was quicker on the herbicide-burn site, with presumably a more rapid return to wetland function. Re-growth at both sites depended upon a pre-existing, diverse soil seed bank. There were no directed changes in soil macroinvertebrate abundance or diversity and they appeared unaffected by changes in the plant community. Phragmites seeds survived only on bare soils, while buried rhizomes survived under all soil conditions. This suggests natural seeding of disturbed soils and inadvertent human planting of rhizomes as likely avenues for Phragmites colonization. Herbicide control, with or without burning, can reduce Phragmites abundance and increase plant biodiversity temporarily. These changes do not necessarily lead to a more diverse animal community. Moreover, unless Phragmites is eradicated and further human disturbance is prohibited, it will likely eventually re-establish dominance.