We used barcoded sequencing to analyze the eukaryotic population in the grape berries at different ripening states in four Australian vineyards. Furthermore, we used an innovative compositional data analysis for assessing the diversity of microbiome communities. The novelty was the introduction of log-ratio balances between the detected genera. Altogether, our results suggest that fungal communities were more impacted by the geographical origin of the Australian vineyards than grape variety and harvest time. Even if the most abundant genera were Aureobasidium and Mycosphaerella, they were ubiquitous to all samples and were not discriminative. In fact, the balances and the fungal community structure seemed to be greatly affected by changes of the genera Penicillium, Colletotrichum, Aspergillus, Rhodotorula, and Botrytis. These results were not evident from the comparison of relative abundance based on OTU counts alone, remarking the importance of the balance analysis for microbiome studies.