In this study we investigated the incidence of Listeria monocytogenes in the receiving meat, the meat products, the personnel and the environment of a vertically integrated company in Northern Greece owing a processing plant and three trading facilities. A total of 303 samples were examined from the receiving raw meat, raw meat preparations, ready-to-eat meat products, processing surfaces and the environment of these facilities as well as the food handlers’ hands and nasal cavities. MALDI-TOF MS was used for Listeria identification; from the 22 (7.26%) positive to Listeria spp. isolates, 12 (3.96%) identified as L. monocytogenes, eight (2.64%) as L. innocua and two (0.66%) as L. welshimeri. Molecular serotyping of L. monocytogenes isolates by multiplex PCR revealed 11 strains belonging to serogroup IIa (1/2a and 3a) and one to IIc (1/2c and 3c). The assay for the detection of the virulence associated genes revealed eight isolates carrying all the examined genes (inlA, inlB, inlC, plcA, prfA, actA, hlyA and iap) and four carrying all except the actA gene. Eleven (91.7%) of the isolates showed strong ability to form biofilm. All isolates were multidrug resistant. The MALDI-TOF Main Spectrum Profile (MSPs), revealed three clusters: one with five isolates (four from environmental samples and one from a food handler), one with five isolates (all from environmental samples), and one with two isolates (both from raw meat products). MALDI-TOF MS seems to be a reliable tool for the identification of niches and contamination routes in processing plants, contributing also to the evaluation and improvement of the applied preventive measures to control L. monocytogenes.