Non-typhoidal Salmonella (NTS) are facultative intracellular pathogens that can promote cell transformation and are associated epidemiologically and experimentally with colon cancer development. Yet, the driving factors of Salmonella-induced cell transformation are mostly unknown. Here, we observed that NTS-associated colon tumors had generally a lower pathological grading suggesting a different biology of the NTS-associated tumors. We studied 30 NTS clinical strains isolated from patients who were later diagnosed with colon cancer >1 year after NTS infection, versus 30 strains from patients who did not develop colon cancer after NTS infection (controls). We characterized these strains for a series of features, including their efficiency to invade and transform mammalian cells, aligned with their genome, transcriptome, and capacity to replicate in various conditions. While the 60 strains displayed diverse infection and transformation efficiencies, case strains showed higher transformation efficiency than matching control strains. Transformation efficiency could not be attributed to specific genomic features, but could be associated with gene expression, particularly metabolic genes and regulons. Moreover, metabolic phenotyping showed that NTS strains with a higher transformation efficiency display increased capacity to utilize various nutrient sources, including carbohydrates and amino acids. Finally, high-transforming NTS strains grow significantly faster intracellularly than low-transforming NTS, using both vacuolar and cytosolic niches. This study highlights the presence of highly transforming NTS within the human population and links transformation efficiency with bacterial transcriptome profile, phenotypic behavior, and intracellular pathogenicity.