The aim of the present work was to evaluate the microbiological quality of chicken thighs after treatment by fennel ( ) and savory ( ) essential oil, stored under vacuum packaging (VP) at 4 ± 0.5 °C for a period of 16 days. The following treatments of chicken thighs were used: Air-packaging control samples (APCS), vacuum-packaging control samples (VPC), vacuum-packaging (VP) control samples with rapeseed oil (VPRO), VP (vacuum-packaging) with fennel essential oil at concentrations 0.2% / (VP + F), and VP with savory essential oil at concentration 0.2% / (VP + S). The quality assessment of APCS, VPC, VPRO, VP + F and VP + S products was established by microbiological analysis. The microbiological parameters as the total viable counts of bacteria of the family, lactic acid bacteria (LAB), and spp. were detected. Bacterial species were identified with the MALDI-TOF MS Biotyper. The combination of essential oils and vacuum packaging had a significant effect ( < 0.05) on the reduction of total viable counts (TVC) compared with control group without vacuum packaging and the untreated control group. Though 15 genera and 46 species were isolated with scores higher than 2.3 from the chicken samples.