Uninoculated wines are regarded as having improved mouthfeel and texture and more complex flavor profiles when compared to wines inoculated with commercial S. cerevisiae strains. Uninoculated fermentation involves a complex microbial succession of yeasts and bacteria during fermentation. Microbial population dynamics are affected by several factors that can ultimately determine if a particular species or strain contributes to wine aroma and flavor. In this work, we have studied the effect of aeration, a common winemaking practice, on the yeast microbiota during uninoculated Chardonnay wine fermentation. The timing of aeration and then aeration intensity were evaluated across two successive vintages. While the timing of aeration significantly impacted fermentation efficiency across oxygen treatments, different levels of aeration intensity only differed when compared to the non-aerated control ferments. Air addition increased the viable cell population size of yeast from the genera Hanseniaspora, Lachancea, Metschnikowia and Torulaspora in both vintages. While in 2019, a high relative abundance was found for Hanseniaspora species in aerated ferments, in 2020, T. delbrueckii was visibly more abundant than other species in response to aeration. Accompanying the observed differences in yeast community structure, the chemical profile of the finished wines was also different across the various aeration treatments. However, excessive aeration resulted in elevated concentrations of ethyl acetate and acetic acid, which would likely have a detrimental effect on wine quality. This work demonstrates the role of aeration in shaping yeast population dynamics and modulating a volatile profile in uninoculated wines, and highlights the need for careful air addition to avoid a negative sensory impact on wine flavor and aroma.