The production of ovine or caprine milk cheeses with thistle rennet is a common practice in the Mediterranean basin, especially in the Iberian and Italian Peninsulas. In these latter geographical areas, numerous Designation of Origin (PDO) or Protected Geographical Indications (PGI) cheeses are traditionally manufactured, including Queijo de Azeitão PDO cheese, produced in Portugal. The aim of the present study was to obtain information on bacteria and yeast communities harboured in Queijo de Azeitão PDO cheese through viable counting and, for the first time, via metataxonomic analyses.Moreover, solid phase microextraction (SPME) technique was applied to characterize Queijo de Azeitão PDO cheese volatile compounds. Cheese wheels were collected from three different artisan producers located in Portugal. Concerning microbiota, a simple composition was shared by the three producers, whose cheese manufactures were dominated by the presence of Leuconostoc mesenteroides, Lactococcus lactis, Lacticaseibacillus zeae, Lentilactobacillus kefiri, Serratia spp., Lactiplantibacillus plantarum, and Lactilactobacillus sakei. The mycobiota composition showed the neat dominance of Yarrowia lipolytica, followed by Candida ethanolica, Kurtzmaniella zeylanoides, Geotrichum candidum, Galactomyces geotrichum, Kluyveromyces lactis, and Geotrichum silvicola. The volatile profile analysis allowed to identify 24 different compounds: 7 acids (acetic acid, isobutyric acid, butanoic acid, 3-methylbutanoic acid, 2methylbutanoic acid, 4-Methyl-2-oxovaleric acid, and hexanoic acid), 7 esters (butyl acetate, ethyl butyrate, propyl butyrate, ethyl exanoate, isopentyl isobutyrate, 2-nonanone, and ethyl octanoate), 4 alcohols (n-propanol, 2-pentanol, 3-Methyl-1-butanol, and 2-heptanol), 3 ketones (2-butanone, 2-pentanone, and 2-heptanone), 2 aromatic hydrocarbons (benzene and toluene), 1 aldehydes (3-methyl-butanal). The most represented volatile organic compounds (VOCs) were 2-butanone, butanoic acid and hexanoic acid. A positive correlation between Lent. kefiri and hexanoic acid and isopentyl isobutyrate was observed. Whereas Y. lipolytica displayed the highest number of positive correlations with 3-methylbutanal, 2-pentanone and 2-pentanol. It is noteworthy that, to the authors' knowledge, this is the very first detection of Lent. kefiri in raw ewe's milk cheese coagulated with vegetable rennet. The presence of Lent. kefiri in Queijo de Azeitão PDO cheese deserves a further in depth, since in kefir, this species, together with L. kefiranofaciens, L. kefirgranum, and L. parakefiri, contributes to the production of health-promoting exopolysaccharides with acknowledged antioxidant, antitumor, antimicrobial, cholesterol reducing and immune-modulating properties. The detection of Lent. kefiri in Queijo de Azeitão PDO cheese represents an absolute novelty, which suggests that this cheese could have still unknown beneficial effects on the health of consumers. Further research is needed to study the dynamics of microbial communities during manufactur...