It is well established, that certain bacteria within the Brochothrix, Carnobacterium, Lactobacillus, Lactococcus, and Leuconostoc genera have an important role in the spoilage of chill stored poultry meat packaged in modified atmosphere. However, little is known about the role of microorganisms that are difficult to culture and the microbiota during poultry spoilage. We combined traditional cultivation and culture-independent 16S rRNA amplicon sequencing to investigate the microbiota encompassing putative bacteria of whole broiler meat, packaged in modified atmosphere, during and exceeding shelf-life. Samples were taken from 6 flocks during independent slaughter days. Additional samples were analysed from the production line. There was a significant difference in the microbial community structure of 80%O ₂ /20%CO ₂ retail packaged broiler meat during different times of shelf-life, mainly due to an increase of species within the Brochothrix, Carnobacterium, Vagococcus, and Janthinobacterium genera. These genera were already detected four to eight days after slaughter. However, no significant difference between flocks with respect to the microbiota encompassing putative spoilage bacteria was observed when examined in retail packaged broilers, slaughtered at the same abattoir on different days. Our study also showed that lactic acid bacteria within the Vagococcus genus can constitute a dominating part of the later shelf-life microbiota in fresh whole broiler meat packaged in 80%O ₂ /20%CO ₂ modified atmosphere. A single operational taxonomic unit (OTU) assigned as Janthinobacterium lividum, an occasional spoiler of meat products, was identified as a major part of the microbiota in late shelf life broiler meat and swab samples in the cooling facility at the slaughter house production line. The combination of traditional cultivation and culture-independent methods provided a great insight into the microbiota of broiler meat during shelf-life and identified a potential point of contamination in the production line for cold tolerant Janthinobacterium.