Introduction and Objective: Salmonella enterica accounts for 80 million cases of foodborne gastroenteritis and 155,000 deaths annually. This study assessed the survival of S. Heidelberg in a gastrointestinal tract (GIT) model and its effects on the metabolome of a stabilized fecal sample. Materials and Methods: Liquid egg and S. Heidelberg (log1011) culture (1:1 ratio) was inoculated into the stomach/small intestine compartment of a modified triple L-SHIME® under parameters mimicking a healthy adult GIT. Samples were collected from the proximal (PC) and distal (DC) colon compartments during a 48-h period. Plate counts were conducted and the profiles of 26 GIT metabolites were characterized using 1H-NMR spectrometry and the Chenomx software. Results: S. Heidelberg decreased from log108.48 to log107.48 (0-h – 12-h) in the PC, and from log107.31 to log106.53 (0-h – 6-h) in the DC compartment. By 48-h, S. Heidelberg decreased to log106.75 (PC) and log105.98 (DC). In the PC compartment, 5 metabolites (4-hydroxyphenylacetate, alanine, formate, methanol, propionate) had significant differences in the majority (at least 5 of the 9) of timepoints. These metabolites (excluding 4-hydroxyphenylacetate) increased in concentration over time when compared to the control. In the DC, 12 metabolites had significant differences in the majority of timepoints. Six of these metabolites (4-hydroxyphenylacetate, alanine, butyrate, cholate, malonate, tryptophan) decreased in concentration over time when compared to the control, while 5-aminopentanoate, formate, glycine, propionate, trimethylamine, and valerate increased in comparison. Conclusion and Significance: S. enterica affects the activity of intestinal microbiota and changes the phenotype of the GIT metabolome.