The semi-dry fermentation processing (SFP) of Coffea arabica is a traditional primary processing method in the coffee industry, which crucially impacts the coffee’s flavor. To further obtain useful information on microbial communities and chemical compounds during the SFP of C. arabica from Yunnan, China, the microbial community structures and the differentially changed non-volatile compounds (DCnVCs) were comprehensively analyzed. The results showed that Tatumella, Staphylococcus, Klebsiella, Brevundimonas, and Gluconobacter were the most prevalent bacteria genera, and Candida, Hannaella, Hanseniaspora, Pichia, and Lachancea were the most abundant fungal genera. Furthermore, 117 DCnVCs were found in the fermentation-finished samples compared to the raw materials. Therefore, this study can provide useful information for understanding the SFP of coffee beans, and its impact on coffee’s quality parameters.