Identifying the soil properties associated with crop yield and quality variation is crucial for developing sustainable agronomic strategies. However, such information on pomelo production is scarce. Hence, forty independent sites in the primary pomelo production areas of Pinghe County were selected to investigate the influence of soil properties on pomelo yield and quality, and to provide reference for future soil management strategies. The results showed positive correlations between pomelo yield and soil pH, along with exchangeable calcium and magnesium, but this comes at the expense of fruit flavor quality. Meanwhile, soil organic matter positively influenced fruit flavor quality. Furthermore, a significant positive effect on fruit nutritional quality was noted across various soil properties, except for organic matter and available phosphorus concentration. A random forest model was used to predict pomelo yield, flavor quality, and nutritional quality based on soil properties and yielded R2 values of 0.50, 0.60, and 0.50, respectively. Partial least squares regression and structural equation modeling identified soil pH and organic matter as pivotal pomelo yield and quality determinants. The categorization of samples into four groups based on differences in pH and organic matter highlighted that integrating soil acidification remediation with organic matter increased is essential for sustainable pomelo production. Overall, this study offers comprehensive insights into the effects of holistic soil management on achieving both high yield and quality in pomelo cultivation. Furthermore, these findings serve as valuable reference for advancing sustainable production practices across large fruit types beyond the pomelo.