Highlights • The naturally regenerated forest had better nutrient status compared with reforestation. • The secondary forest and Eucalyptus plantation had higher carbon substrates use efficiencies than the Pinus yunnanensis plantation. • The indicators selection method of Minimum Data Set can adequately represent the Total Data Set method. • The natural regeneration may be a more effective approach to the amelioration of soil quality in the karst areas. Abstract Natural regeneration and reforestation have been widely adopted to improve the degraded soil and promote ecological services in the karst regions of southwestern China. A better understanding the effects of different vegetation types on soil quality and the nutrient limiting factors is very important for each approach. In this study, a secondary forest (SF) and two plantations, Eucalyptus maideni F. V. Muell. (EM, exotic, deciduous broad-leaved) and Pinus yunnanensis Franch. (PY, native, conifer species), were selected in the karst graben basins of southwest China to explore the soil quality using Total Data Set (TDS) and Minimum Data Set (MDS) methods. The results indicated most soil parameters showed significant differences between the different recovery approaches. The TDS method is more precise than the MDS method, but the MDS method can also adequately represent the TDS method for the evaluation of soil quality with different vegetation restoration schemes. In the MDS method, soil organic carbon, available potassium, ammonium nitrogen, acid phosphatase, microbial metabolic quotient, and the Pielou index of the soil microbes were found to be the most important indicators for assessing soil quality. The pure plantation of PY had a negative effect on the soil quality, causing soil nutrient deficiency, compared to the SF and EM plantation, indicating that natural regeneration may be a more effective approach to the amelioration of soil quality in the karst areas. These findings provide an empirical and theoretical basis for the protection, restoration, and management of forest in the degraded karst areas. [ABSTRACT FROM AUTHOR]