Colorectal cancer (CRC) is one of the most common cancers with high morbidity and mortality. The modulation of intestinal health through the administration of pro- and prebiotics may be a viable alternative to reduce the risk of CRC. This study aimed to evaluate the functional effects of yacon and kefir, isolated or associated, in rats with colorectal cancer. Adult Wistar rats were divided into five groups (n = 8): HC (healthy control AIN-93M diet), CC (CCR + AIN-93M diet), Y (CCR + AIN-93 M + yacon diet), K (CCR + AIN-93-M + kefir diet) and YK (CCR + AIN-93 M + yacon + kefir diet). Colorectal carcinogenesis was induced in groups CC, Y, K, and YK with 1,2-dimethylhydrazine (55 mg kg-1, subcutaneously) for 5 weeks. From the 6th week onwards, the experimental groups were fed the respective diets. In the 15th week, urine was collected for analysis of intestinal permeability and then the animals were euthanized. Yacon increased acetate levels, reduced pH and carcinogenic neoplastic lesions, and increased the abundance of bacteria related to the fermentation of non-digestible carbohydrates, such as the genera Dorea, Collinsela, and Bifidobacteria. On the other hand, kefir increased macroscopic neoplastic lesions and increased the abundance of Firmicutes and Clostridium. The association of yacon + kefir increased the number of carcinogenic lesions, despite a reduction in pH and beneficial bacteria prevalence. Thus, it is concluded that yacon, unlikely kefir, is a promising alternative to mitigate the manifestations of induced carcinogenesis in rats.