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Coffee is one of the most valuable agricultural commodities worldwide, second only to oil in terms of international trade. Coffea arabica L. is a widely cultivated and economically important crop that is responsible for about 90% of the global production of coffee. In this study, we selected five C. arabica cultivation sites at different altitudes to clarify the effects of altitude on rhizospheric soil physical–chemical characteristics and microbial communities. The samples collected at low altitudes were more nutrient-deficient and acidic than the soil samples collected at medium–high altitudes. The Proteobacteria-to-Acidobacteria ratio increased from lower altitudes to medium–high altitudes. Additionally, although Ascomycota was the dominant fungal phylum, it was unaffected by the altitude. Furthermore, the alpha richness and diversity of the bacterial and fungal communities were higher at medium–high altitudes than at low altitudes. Moreover, the redundancy analysis indicated that microbial phyla were closely associated with pH. These findings suggest that C. arabica should be cultivated at medium–high altitudes, which is conducive to sustainable management and the production of high-quality C. arabica beans.