Multi-omics approaches and advances in high-throughput sequencing (HTS) methods transformed the understanding of cheese microbiology. Sequencing of total DNA, RNA, proteins, metabolites permit to make description and to establish which components are responsible for the authentic taste and flavors. Bitterness is a common flavour frequently detected in many cheese technologies. Proteins fractionation resulting in bitter peptides is caused by rennet addition, proteases produced by starter or non-starter microbial communities and milk proteases. Bitterness may be due to specific amino acids in a terminal peptide position or milk derived bioactive peptides. Blue-veined cheeses are regularly described as bitter but links between microbial diversity, function, gene expression and bitterness are not always well-understood. In the present work, we combined microbiological, biochemical, metabarcoding (amplicon sequencing), metagenomic (DNA-Seq) and metatranscriptomic (RNA-Seq) conjugated to physico-chemical and sensorial analyses to better understand the origins of excessive bitterness in French blue-veined PDO Bleu d’Auvergne cheeses.