The role of microbial diversity in influencing the organoleptic properties of wine and other fermented products is well est ablished, and understanding microbial dynamics within fermentation processes can be critical for quality assurance and product innovation. This is especially true for winemakers using spontaneous fermentation techniques, where environmental factors may play an important role in consistency of product. Here, we use a metabarcoding approach to investigate the influence of two environmental systems used by an organic winemaker to produce wines; vineyard (outdoors) and winery (indoors) to the bacterial and fungal communities throughout the duration of a spontaneous fermentation of the same batch of Pinot Noir grapes. Bacterial (RANOSIM= 0.5814, p = 0.0001) and fungal (RANOSIM= 0.603, p = 0.0001) diversity differed significantly across the fermentation stages in both systems. Members of theHyphomicrobiumgenus were found in winemaking for the first time, as a bacterial genus that can survive alcoholic fermentation. Our results also indicate thatTorulaspora delbrueckiiandFructobacillusspecies might be sensitive to environmental systems. These results clearly reflect the substantial influence that environmental conditions exert on microbial populations at every point in the process of transforming grape juice to wine via fermentation, and offer new insights into the challenges and opportunities for wine production in an ever-changing global climate.