Recent studies underscore the pivotal role of microbial terroir in shaping coffee fermentation and quality. However, the specific influence of regional microbiomes on flavor development remains underexplored. This study explored the link between the coffee farm microbiome and the resulting spontaneous fermentation process in Brazil's Atlantic Forest and Semi-arid Cerrado biomes. Using Illumina-based amplicon sequencing, 972 prokaryotes and 435 eukaryotes were identified from coffee fruits, leaves, depulped coffee beans, over-ripe beans, soil, and temporal fermentation samples. During the fermentation process, microorganisms present in the pulped fruit (viz., Leuconostoc and Kazachstania) were the main microbial groups driving fermentation process across the two biomes, leading to the accumulation of primary (ethanol and lactic acid) and secondary (esters, aldehydes, higher alcohols, and ketones) metabolites. However, Leuconostoc and Kazachstania communities were significantly higher in the pulped fruit samples from the Atlantic Forest compared to the Cerrado biome. Therefore, the Atlantic Forest farm showed more stable microbial dynamics during the fermentation process and the formation of key flavor metabolites, such as methyl salicylate, linalool, ethyl linoleate, benzeneacetic acid ethyl ester, and phenylethyl alcohol. In contrast, the Cerrado samples exhibited higher microbial richness, leading to the emergence of co-dominant species such as Pantoea, Cutaneotrichosporon, Hyphopichia, Wickerhamomyces, and Cladosporium. Sensory evaluation revealed higher overall scores for the Atlantic Forest coffee, characterized by fruity, floral, and caramel notes, compared to earthy and herbal characteristics of Cerrado coffee. The findings demonstrate the influence of terroir-driven microbial communities on coffee fermentation and coffee quality, providing insights into optimizing fermentation for enhanced coffee flavor development and contributing to the growing field of microbial-assisted coffee production.