The production of traditional agave spirits in Mexico, such as mezcal, involves a process that uses environmental microorganisms to ferment the cooked must from agave plants. By analysing these microorganisms, researchers can understand the dynamics of microbial communities at the interface of natural and human‐associated environments. This study involved 16S and ITS amplicon sequencing of 99 fermentation tanks from 42 distilleries across Mexico. The Agave species used, production methods, climatic conditions and biogeographic characteristics varied significantly among sites. However, certain taxa were found in most fermentations, indicating a core group of microorganisms common to these communities. The primary variable consistently associated with the composition of both bacterial and fungal communities was the distillery, suggesting that local production practices and site‐specific attributes influence the microbiomes. The fermentation stage, climate and producing region also affected community composition but only for prokaryotes. Analysis of multiple tanks within three distilleries showed taxa enriched in specific fermentation stages or agave species. This research provides a detailed analysis of the microbiome of agave fermentations, offering important knowledge for its management and conservation. [ABSTRACT FROM AUTHOR]

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