In this study, an amplicon metagenomic approach was used to determine the effect of repeated treatments with ozonized oleic acid on the microbial community of grapevine carpoplane. Differences in community composition of treated vineyards were compared to non-treated and conventionally treated samples regarding the prokaryotic and eukaryotic microbiome at two developmental stages (BBCH 83, BBCH 87). The results showed effects both on occurrence and on abundance of microorganisms and the community assembly. Wine-relevant genera such as Acetobacter and members of the former genus Lactobacillus could be identified as part of the natural microbiota. The impact of the new viticultural treatment on these organisms was assessed in liquid culture-based microtiter assays. Therefore, we investigated an array of two acetic acid bacteria (AAB), four lactic acid bacteria (LAB) and nine saccharomyces and non-saccharomyces yeasts. Brettanomyces bruxellensis, Saccharomyces cerevisiae, Pediococcus sp. and Acetobacter aceti revealed the highest sensitivities against ozonized oleic acid (LIQUENSO® Oxygenat). Culture growth of these organisms was significantly reduced at an ozonide concentration of 0.25% (v/v), which corresponded to a quarter of the concentration used in the vineyard. The metabarcoding approach in combination with complementary in vitro assays allow new insights into treatment effects on the community and species scale.