Colorectal cancer is one of the most invaded lethal types of malignancy worldwide. It's an important issue to find prophylactic and curative agents against that life-threatening ailment, preferably from cheap, natural, commonly available nutraceuticals. Herein, total pomegranate peel extract was tested for its significance as an anticancer agent against bacterial pathogens-induced colon cancer in mice model. The phytochemical investigation was carried out via quantitative estimation of phenolic and flavonoid contents along with metabolomic analysis. In this study, Bagg Albino/c (BALB/c) mice were classified into 4 groups including negative control group, untreated mice with pathogen-induced colon cancer group, mice treated with 5-flurouracil and mice treated pomegranate peels extract (PPE). B cell lymphoma gene 2 (BCL2) and hypoxia-inducible factor 1 -α (HIF1-α) proteins were measured using enzyme-linked immunosorbent assay (ELISA) kits in all groups. Histopathological changes occurred in the colon of 4 groups were evaluated. The bioactive extract was found to possess a potent antioxidant capacity (357.6 ± 0.5 and 408.4 ± 0.55 mg Trolox equivalents/g) for 1, 1-Diphenyl-2-picryl-hydrazyl (DPPH) and 2, 2‵-azinobis-3-ethylbenzothiazoline-6-sulfonate (ABTS) assays, respectively, owing to its high amount of phenolic acids (174.0±0.65) mg gallic acid equivalent/g and flavonoids (23.2 ±0.3 mg catechin equivalent/g). Furthermore, metabolomics investigation by liquid chromatography/electrospray ionization - tandem mass spectrometry (LC-ESI-MS/MS) analysis revealed the identification of 73 metabolites from varying chemical classes, most abundantly gallotannin and ellagitannin derivatives, flavonoids and their glycosides, pentacyclic triterpenes, coumarins, in addition to many phenolic and fatty acids. In vivo experiment, the metabolomics investigation by gas chromatography - mass spectrometry (GC-MS) revealed a decrease in 1H-indole-3-acetic acid and heptanedioic acid in mice treated PPE compared with untreated mice with pathogen-induced colon cancer group. Moreover, an increase in benzoic acid, alanine, phenylalanine, and glucose were observed in mice treated PPE compared with untreated mice. Finally, reduction in of BCL2 and HIF1-α serum levels in treated groups compared to untreated group. PPE showed anticancer activity against bacterial pathogen-induced colon cancer in vivo via reduction of serum levels of BCL2 and HIF1-α as apoptosis controlling factors leading to histopathological improvement of colon of PPE treated group.