Increasing reports onK. pneumoniaestrains with antimicrobial resistance and virulence traits from food and farm animals are raising concerns about the potential role ofKlebsiellaspp. as a foodborne pathogen. This study aimed to report and characterizeKlebsiellaspp. isolates from two artisanal ready-to-eat food (soft cheese and salami) producing facilities, and to track similar genotypes in different ecological niches. Over 1170 samples were collected during the whole production chain of different food batches. The overallKlebsiellaprevalence was 6%. Strains were classified into the threeKlebsiellaspecies complexes:K. pneumoniae(KpSC, n = 17),K. oxytoca(KoSC, n = 38) andK. planticola(KplaSC, n = 18). Despite high genetic diversity we found in terms of known and new sequence types (STs), core genome phylogeny revealed clonal strains persisting in the same processing setting for over 14 months, isolated from the environment, raw materials and end-products. Strains showed a natural antimicrobial resistance phenotype-genotype.K. pneumoniaestrains showed the highest virulence potential, with sequence types ST4242 and ST107 strains carrying yersiniabactinybt16and aerobactiniuc3. The latter was detected in allK. pneumoniaefrom salami and was located on a large conjugative plasmid highly similar (97% identity) toiuc3+plasmids from human and pig strains circulating in nearby regions of Italy. While identical genotypes may persist along the whole food production process, different genotypes from distinct sources in the same facility shared aniuc3-plasmid. Surveillance in the food chain will be crucial to obtain a more comprehensive picture of the circulation ofKlebsiellastrains with pathogenic potential.