A detailed understanding of the microbial ecology of artisanal cheeses is a crucial factor for implementation practices that can help to update their quality. In this study, the bacterial communities of Protected Designation of Origin (PDO) ‘Queso de la Serena’ and ‘Torta del Casar’ cheeses were characterised by 16S rRNA gene metabarcoding sequencing over 60 days of ripening at three dairies for each cheese variety. Both PDO cheeses presented a distinctive and unique bacterial community, suggesting that the manufacturing practices of each PDO shaped the microbiota. Lactococcus lactis and, to a lesser extent, Leuconostoc mesenteroides were the key lactic acid bacteria (LAB) species that drove the ripening process of PDO ‘Torta del Casar’, whereas in PDO ‘Queso de la Serena’, Leu. mesenteroides was the main LAB species, followed by Lactococcus raffinolactis and Lc. lactis, depending on the dairy. Furthermore, a wide range of non-starter LAB, Gram-negative bacteria and Gram-positive catalase-positive cocci were found, with a variable presence and abundance between dairies. In this regard, the dairy was a strong contributing factor to the variability in the composition of the bacterial community in each cheese type. In contrast, the impact of the ripening process was limited. Overall, this study enhances the understanding of the bacterial dynamics that occur during the ripening of these traditional PDO cheeses, highlighting the need to improve the standardisation of the raw materials and manufacturing practices to minimise inter-dairy variability, ensuring final quality and their unique sensory traits. •Bacterial diversity of Queso de la Serena and Torta del Casar PDO cheeses was studied.•A 16S rRNA gene metabarcoding sequencing approach was applied.•Lactococcus lactis and Leuconostoc mesenteroides were the predominant species.•Each PDO cheese can be defined by a unique and distinctive bacterial profile.•Bacterial community composition is affected by dairy manufacturing practices.