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The aim of the present study was to assess the influence of ripening container’s material on the bacterial diversity of Feta cheese PDO (Protected Designation of Origin). The microbiota of fresh and mature cheese produced in plastic and stainless steel container was monitored by microbial enumeration and 16s rRNA gene sequencing. According to the obtained results, lactic acid bacteria (LAB) was the dominant microbiota of fresh and mature cheese. Metagenomics data revealed that fresh cheese was dominated by <i>Lactococcus</i> followed by members of <i>Enterobacteriaceae</i> family and <i>Pseudomonas</i>. Similarly, <i>Lactococcus</i> was the most abundant genus detected in mature cheese (54 days and 120 days), regardless of the container’s material. In both fresh and mature cheese, species of <i>Pseudomonas</i>, <i>Streptococcus</i>, <i>Acinetobacter</i>, <i>Lactobacillus</i>, <i>Flavobacterium</i>, and <i>Carnobacterium</i> were detected. The abundance of <i>Enterobacteriaceae</i>, <i>Moraxellaceae</i> and <i>Pseudomonadaceae</i> in mature cheese ripened in stainless steel container seems to be numerically reduced after 120 days of storage compared to the cheese ripened in plastic container but not significant differences were observed (<i>p</i> &gt; 0.05). In conclusion, metagenomic analysis suggests that ripening container’s material does not affect the microbial community responsible for the ripening of feta cheese PDO.