| Summary: | Coffee fermentation is crucial for flavor and aroma, as microorganisms degrade mucilage and produce metabolites. This study aimed to provide a basis for understanding the impact of microorganisms on <i>Coffea arabica</i> from Yunnan, China, during washed processing. The microbial community structure and differentially changed metabolites (DCMs) of <i>C. arabica</i> beans during washed processing were analyzed. The results indicated that the top five predominant microorganisms at the genera level were <i>Achromobacter</i>, <i>Tatumella</i>, <i>Weissella</i>, <i>Streptococcus</i>, and <i>Trichocoleus</i> for bacteria and <i>Cystofilobasidium</i>, <i>Hanseniaspora</i>, <i>Lachancea</i>, <i>Wickerhamomyces</i>, and <i>Aspergillus</i> for fungi. Meanwhile, the relative content of 115 DCMs in 36 h samples decreased significantly, compared to non-fermentation coffee samples (VIP > 1, <i>p</i> < 0.05, FC < 0.65), and the relative content of 28 DCMs increased significantly (VIP > 1, <i>p</i> < 0.05, FC > 1.5). Furthermore, 17 DCMs showed a strong positive correlation with microorganisms, and 5 DCMs had a strong negative correlation (<i>p</i> < 0.05, |r| > 0.6). Therefore, the interaction and metabolic function of microbiota play a key role in the formation of coffee flavor, and these results help in clarifying the fermentation mechanisms of <i>C. arabica</i> and in controlling and improving the quality of coffee flavor.
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