Natural forests tend to be converted into agricultural lands in developing countries for economic development. In the subtropical regions of China, natural secondary forests are generally converted to banana, rubber, and eucalyptus plantations. Unlike natural forests, agricultural lands are mainly characterized by mono-plantations, tillage, fertilization, and litter removal. These practices may have unfavorable consequences on the soil ecosystem. Moreover, the soil in the subtropical regions of China is classied as Ultisol, which is vulnerable to erosion and degradation under improper soil management. Yet, knowledge about the effects of the conversion of natural forests to agricultural lands on soil quality in these regions remains scarce. Soil microorganisms are critical for organic matter conversion and nutrient cycling, in addition to being sensitive to environmental changes. Thus, soil microbial parameters such as microbial biomass, activity, biodiversity, and composition are considered as reliable indicators of soil quality. To understand the effect of forest conversion to agricultural lands on soil microbial parameters, as well as soil chemical properties, we collected soil samples from a well-conserved natural secondary forest, in addition to transformed banana, eucalyptus, and rubber forests. Phospholipid fatty acid (PLFA) analysis, denaturing gradient gel electrophoresis (DGGE), and community-level physiological profiles (CLPP) were used to investigate various microbial parameters, including microbial biomass, activity, community diversity, and functional diversity. Microbial diversity was expressed as Shannon diversity (H'). Principal component analysis (PCA) was performed to analyze the soil microbial structure based on PLFA, CLPP, and DGGE data. In addition, soil chemical properties were determined, including pH, organic carbon, available nitrogen, total phosphorus, available phosphorus, and available potassium. Stepwise multiple regression analysis was used to determine the main soil properties that influenced soil microbial parameters. The results showed that the natural secondary forest had the highest total PLFA, which was 3 and 2 times higher than that recorded for the banana and rubber forests, respectively. The average color development (AWCD), community diversity, and functional diversity determined from the PLFA, DGGE, and CLPP profiles were also highest in the natural secondary forest. Soil microbial community structure differed between the natural secondary forest and agricultural lands, as well as between the vegetation types. In addition, soil pH, organic carbon, total nitrogen, total phosphorus, available nitrogen, and available potassium were higher in the natural secondary forest compared to the agricultural lands. The stepwise analysis showed that soil pH and available phosphorus affected H' and CLPP values, while organic carbon affected AWCD, H' of fungal DGGE, and fungal biomass values. Total nitrogen and available nitrogen generally affected microbial biomass (total, bacterial, and fungal PLFAs) and community diversity (H' of DGGE and PLFA data). Our results indicate that the conversion of natural secondary forests to agricultural lands leads to soil acidification and a significant decrease in soil organic carbon and nutrient content. Furthermore, conversion decreases microbial biomass, activity, diversity, and functional diversity, causing shifts in soil microbial community structure. The adverse effects of this conversion on soil chemical and microbial properties may be due to the agricultural management practices being followed at local sites.