Bauxite residue disposal areas may be amended and re-vegetated to facilitate the ecosystem restoration process. However, the development of the belowground system during restoration is frequently overlooked. In turn, although vegetation establishment on bauxite residue is well studied, virtually nothing is known about concurrent changes in the soil biota. In order to understand how different amendments and re-vegetation influence the belowground community, we compared nematode assemblages from bauxite residues that differed in their treatment history (compost addition, gypsum addition, and time since re-vegetation), and examined whether any differences were related to changes in soil properties. No nematodes were present in the unamended treatment, thus indicating a need for amelioration of substrate properties. However, there were differences in the nematode assemblage between the other amended treatments. The quantity of gypsum reduced nematode density, but had no effect on taxa richness or the Maturity Index in treatments amended in the same year. Nematode taxa richness and the Maturity Index were greatest in the treatment re-vegetated earliest. Moreover, the Maturity Index was negatively correlated to soil pH and percentage Na. These findings indicate that sufficient amendment and re-vegetation are crucial to address inhibitory characteristics of the residue and aid restoration of the belowground system in bauxite residues.