| Summary: | The poultry industry in Colombia has implemented several changes and measures in chicken processing to improve sanitary operations and control pathogens’ prevalence. However, there is no official in-plant microbial profile reference data currently available throughout the processing value chains. Hence, this research aimed to study the microbial profiles and the antimicrobial resistance of <i>Salmonella</i> isolates in three plants. In total, 300 samples were collected in seven processing sites. Prevalence of <i>Salmonella</i> spp. and levels of Enterobacteriaceae were assessed. Additionally, whole-genome sequencing was conducted to characterize the isolated strains genotypically. Overall, the prevalence of <i>Salmonella</i> spp. in each establishment was 77%, 58% and 80% for plant A, B, and C. The mean levels of Enterobacteriaceae in the chicken rinsates were 5.03, 5.74, and 6.41 log CFU/mL for plant A, B, and C. Significant reductions were identified in the counts of post-chilling rinsate samples; however, increased levels were found in chicken parts. There were six distinct <i>Salmonella</i> spp. clusters with the predominant sequence types ST32 and ST28. The serotypes Infantis (54%) and Paratyphi B (25%) were the most commonly identified within the processing plants with a high abundance of antimicrobial resistance genes.
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