Colorectal Cancer (CRC) is the third most diagnosed type of cancer worldwide. Prebiotics containing Fructooligosaccharides (FOS) and inulin have been reported to improve CRC in experimental models. We hypothesized whether consumption of the yacon-based product (PBY-Smallanthus sonchifolius concentrate), as a source of FOS and inulin, could mitigate colonic pre-neoplastic lesion development in mice by enhancing fecal Short-Chain Fatty Acid (SCFA) production besides modulating intestinal immune responses. Therefore, we investigate the effects of PBY consumption on anatomical and fecal characteristics, serum biomarkers, fecal SCFA concentration, intestinal lymphocytes population, expression of transcription factors of the adaptive immune response and Aberrant Crypt Foci (ACF) count in the colon of mice chemically induced to pre-neoplastic lesions. Male BALB/c mice were injected intraperitoneally with 1,2-dimethylhydrazine (20mg/kg body weight/week) for 8 weeks. Thereafter, mice were fed either control (AIN-93M) or PBY diet (AIN-93M supplemented with PBY, 6.0% FOS +Inulin) for 8 weeks and then euthanized. PBY was not successful in reducing ACF counts; however, it improved fecal SCFA concentration (formic, acetic, propionic, butyric and valeric), reduced fecal pH and increased humidity and viscosity of feces. Although there were no significant changes in the intestinal lymphocytes population (CD4, CD8, Natural Killer, Treg and Th17), PBY consumption modulates the immune response in the colon reducing the expression of FOXP3 and increasing RORγt and T-bet, which would contribute to activation and proliferation of CD8 T lymphocytes and better CRC prognosis. Therefore, we suggest that PBY might improve intestinal health during the early stages of colorectal carcinogenesis, especially by modulating SCFA production and colonic adaptive immune response.