Microbial communities underpin the safety, consistency, and functional properties of fermented foods; however, traditional culture-based methods can result in poorly characterized communities across manufacturers and batches. Molecular approaches enable rapid, cultivation-independent profiling of microbial community composition and function. To gain deeper insights into microbial communities, high-throughput metabarcoding was applied to characterize bacterial and fungal communities in fermented plant-based drink concentrates from seven European manufacturers. Samples were collected at two time points representing independent batches. Bacterial and fungal communities were profiled using 16S rRNA gene and internal transcribed spacer 2 (ITS2) amplicon sequencing, respectively. Taxonomic profiles were complemented by functional assessment to flag beneficial taxa associated with fermentation and taxa with potential spoilage or safety relevance. Bacterial communities were dominated by lactic acid bacteria, including Lactobacillus spp. (e.g., L. acidophilus), Leuconostoc spp., and Lactococcus spp., alongside probiotic genera such as Bifidobacterium spp. Low-abundance sequences assigned to taxa with potential safety relevance, including Clostridium perfringens, were detected. Fungal communities were dominated by the fermentative yeast Saccharomyces spp., alongside environmental taxa such as Fusarium, some of which may have mycotoxin-producing potential. Community composition varied by manufacturer and batch for both bacteria and fungi; however, manufacturer effects were substantially stronger for bacterial communities, explaining 74.8% of bacterial variance compared to 35.4% for fungi. These findings indicate that metabarcoding with functional assessment can serve as an initial flagging system for routine microbial monitoring and enables tracking of community composition and consistency across batches and markets, thereby improving quality insights in fermented food production.