Rare earth element (REE) mining has wrought severe ecosystem destruction, particularly in the loss of carbon (C), nitrogen (N), and phosphorus (P). Furthermore, its effects on nutrient recovery characteristics and associated microbial abundance are still poorly understood. In this study, an investigation was conducted to determine C, N, and P recovery patterns and microbial communities in abandoned REE mining tailings with different abandoned durations of 1.5 (1.5-Y), 7 (7-Y), 10 (10-Y), and 14 (14-Y) years and at an unmined site (the control group) in Jiangxi Province, China. Longitudinal tailing delamination at each site was investigated in 0–15 (layer 1) and 15–30 (layer 2) cm tailing layers. During the abandoned duration of REE tailings, C and P in layer 1 continued to recover from 1.62 to 8.51 g kg-1 and from 0.71 to 1.94 g kg-1, respectively; N losses of 0.60 and 0.22 g kg-1 occurred at the 1.5-Y and 10-Y sites, while N in layer 1 slightly increased at the 14-Y site. Mesorhizobium, Methylosinus, Bradyrhizobium, Pseudomonas, and Azospirillum were dominant bacteria at the 14-Y site and in the control. The relative abundances of N-fixing bacteria Mesorhizobium (32.94%), Sinorhizobium (0.24%), Frankia (0.71%), and Burkholderia (2.38%) at the 14-Y site were 1.33–3.97 times those in the control (24.19%, 0.18%, 0.32% and 0.60%, respectively), which was helpful for tailing N recovery. At the 14-Y site, Tylospora (50.24%), Luellia (11.02%), Tomentella (6.94%), and Chaetomium (4.34%) were the dominant fungal genera, while Tylospora (56.93%), Suillus (11.45%), and Penicillium (6.78%) predominated in the control. The relative abundance of the P-dissolving fungus Aspergillus at the 14-Y site (0.42%) was 4.2 times that in the control (0.1%), which may lead to the improved tailing P solubility. At the 14-Y site, woody plants such as Pinus massoniana and native pioneering herbs and ferns such as Dicranopteris dichotoma and Nephrolepis auriculata probably invaded from adjacent areas. This study unraveled the natural restoration of plant and microbial communities along with soil nutrient changes in abandoned REE tailings, thus providing a novel insight into ecological recovery and restoration after mining.