Vegetation restoration is assumed to enhance carbon (C) sequestration in terrestrial ecosystems, where plant producers and microbial decomposers play key roles in soil C cycling. However, it is not clear how the nutrient limitation patterns of plants and soil microbes might change during vegetation restoration. We investigated the nutrient limitations of the plant and microbial communities along a natural vegetation restoration chronosequence (1, 8, 16, 31, and 50 years) following farmland abandonment in Qinling Mountains, China, and assessed their relationships with soil factors. The result showed that following natural vegetation restoration, the nitrogen (N) limitation of plant and microbial communities was alleviated significantly, and thereafter, it began to shift to phosphorus (P) limitation at a later stage. Plants showed P limitation 50 years after restoration, while microbial P limitation appeared 31 years later. The changes in plant nutrient limitation were consistent with those in microbial nutrient limitation, but soil microbes were limited by P earlier than plants. Random forest model and partial least squares path modeling revealed that soil nutrient stoichiometry, especially soil C:N ratio, explained more variations in plant and microbial nutrient limitation. Our study demonstrates that the imbalanced soil C:N ratio may determine the soil microbial metabolic limitation and further mediate the variation in plant nutrient limitation during natural vegetation restoration, which provides important insights into the link between metabolic limitation for microbes and nutrient limitation for plants during vegetation restoration to improve our understanding of soil C turnover in temperate forest ecosystems.