Forest ecosystem productivity and function is strongly influenced by the interaction between soil organisms and their resource use that can be impeded by an imbalance of ecological stoichiometry. Soil microbial communities are known to have an important role in biogeochemical cycling that is strongly influenced by ecological stoichiometry; however, there is limited understanding of how soil biota respond to stoichiometric imbalances during forest restoration. Here, we investigated the effect of forest restoration on soil physiochemical properties and the structure and function of soil biota along a chronosequence of transformation stages: (i) an early stage monoculture plantation of Chinese fir (Cunninghamia lanceolata) comprised of three age classes (5, 10, 20 years); (ii) mid-stage mixed conifer-broadleaved forest; and (iii) late-stage mixed species broadleaved forest in south China. The abundance and community composition of soil bacteria, fungi, protists and nematodes were investigated by real-time quantitative PCR and Miseq high-throughput sequencing. Results showed that forest restoration from C. lanceolata monocultures to mixed species broadleaved forest significantly increased soil organic carbon and total nitrogen concentration. The abundance of soil bacteria, fungi, protists and nematodes increased and the co-occurrence networks of soil biota became more complex and stable along the restoration chronosequence. In contrast, the soil nitrogen and phosphorus limitations, particularly phosphorus limitation, increased along the restoration chronosequence, and soil exoenzyme activity suggested that the microbial investment in resource acquisition shifted from C- to nutrient-acquiring enzymes from the earlier to the later restoration stages. Availability of soil resources (e.g., dissolved organic carbon, ammonium, and plant available phosphate) appeared to have an important role in regulating soil food web composition, structure and stability during forest restoration. We conclude that nutrient limitation, particularly phosphorus limitation, likely has an important role in determining the stability of soil food webs during forest restoration. These findings contribute to our understanding of the relationships between soil nutrient limitation and soil micro-food web, and have implications for carbon sequestration through forest restoration and management in southern China.