Salmonellosis is a major public health concern with a significant cost in many countries. Imposed by an increasing prevalence of multi-drug resistant strains, biological alternatives for the treatment of Salmonella infections are needed. We combined two original in vitro models closely mimicking the complex in vivo intestinal situation to investigate the therapeutic potential and mechanisms of two promising bacteriocinogenic probiotics, Bifidobacterium thermophilum RBL67 (thermophilicin B67) and Escherichia coli L1000 (microcin B17-producer), active against Salmonella. A recently developed continuous three-stage colonic fermentation model of S. Typhimurium infection with immobilized child fecal microbiota was used to simulate the proximal, transverse and distal human colonic sections. Reactor effluents were directly applied to intestinal mucus-secreting HT29-MTX cell-layers to measure first-level host responses after induction of infection and probiotic treatments. Stable pathogen invasion into HT29-MTX cells (1 ± 0.4%) was recorded after infection accompanied by decreased epithelium integrity (45% lower Trans Epithelial Electrical Resistance compared to non-infected control). After adding E. coli L1000, Salmonella invasion only decreased in the distal reactor (89%) while TEER did not change for all samples. In contrast, anti-Salmonella activity of B. thermophilum RBL67 was most pronounced in the proximal reactor with a 76%-decrease of pathogen invasion and TEER recovered close to levels of non-infected samples. Bio-Plex (Bio-Rad) analysis was used to measure cellular immune responses. Our results highlight the benefits to combine suitable cellular and colonic fermentation models to evaluate host protection activity of probiotics during Salmonella infection, providing efficient tools for mechanistic studies and preclinical development of new antimicrobials.