Over-exploration of rare earth elements causes soil desertification and environmental degradation. However, the restoration of rare earth mine tailings requires the recovery of both vegetation and soil microbiota. Accordingly, the present study aimed to compare the efficacy of restoring mine tailings using organic compost and native plants (Miscanthus sinensis, Pinus massoniana, Bambusa textilis, or a mixture of all three). After three years, the mixed plantation harbored tenfold greater plant richness than that in the barren land. Among these, M. sinensis played a dominant role across all restored areas. The microbial communities of the soils were assessed using high-throughput 16S rDNA gene sequencing. A total of 34,870 16S rDNA gene sequences were obtained and classified into 15 bacterial phyla and 36 genera. The dominant genus across all the restored soils was Burkholderia, and the bacterial diversity of restored soils was greater than that of soils from either unrestored or natural (unexploited) areas, with the M. sinensis plantation yielding the greatest diversity. The effects of phytoremediation were mainly driven by changes in nutrient and metal contents. These results indicate that M. sinensis significantly improves phytoremediation and that mixed planting is ideal for restoring the soils of abandoned rare earth mines.