Grape berries host a complex microbial community that plays a predominant role in grape quality prior to harvest and in the winemaking process. Like other carpospheric habitats, the epiphytic microbial community of grape berries is influenced by several factors. Climate plays an essential role in grape composition and quality, and its impact on berry microbiota was recently demonstrated. However, there is still a lack of information about how environmental conditions influence the system in grape berries. In this study, the microbial communities of grape berries from two wine appellations characterized by specific climatological conditions were analyzed. The results revealed that the size of cultivable communities (bacteria, yeast and filamentous fungi) and the diversity and richness of the microbial community profiles were higher in vineyards found to have lower temperatures. The metabolic activity (Community-Level Physiological Profiles) of the epiphytic microbial community was lower in warm climates. Water activity (aw) had a positive effect on the cultivable population, on metabolic activity, and on microbial diversity. The results showed that the microclimate affects the microbial population associated with grape berries through the aw of grape skins.