Abstract: Taking Kunming wrinkled-skinned pepper as the test object, a total of 11 treatments, including single application and mixed application of microbial fertilizers, were set up to explore the effects of applying different microbial fertilizers at different growth stages on physicochemical properties and enzyme activity of pepper-growing soil. The results showed that the addition of microbial fertilizers significantly enhanced soil nutrient content and enzyme activity. The mixed fungal fertilizer treatments enhanced soil nutrients and enzyme activities better than the single fungal fertilizer treatments. The effect was more obvious in both the flowering period and the fruit-bearing period than in the seedling stage. There was a significant or extremely significant correlation between soil nutrient content and enzyme activity. The soil nutrient indicators that have a greater impact on soil enzyme activity are available potassium, available phosphorus, and organic matter. The DG treatment (20 g compound bacterial fertilizer + 30 mL photosynthesis bacterial fertilizer) was effective in enhancing soil nutrient content and enzyme activity and it is recommended to promote the application of chili peppers in the cultivation and production practice.