Promising results from different studies on the effect of probiotics in cancer prevention and therapy have so far been reported. However, the molecular mechanism of the interaction of probiotics with cancer cells is yet to be fully understood. In the present study, Leuconostoc mesenteroides was isolated from traditional dairy products, and its probiotic characteristics were determined. HT-29 cells were treated with conditioned-medium of designated bacteria and the cell apoptosis was studied at cellular and molecular level using DAPI staining, flow cytometry, DNA ladder assays, and real-time quantitative-PCR (q-PCR). Based on our findings, L. mesenteroides promoted apoptosis in colon cancer cell line by upregulation of MAPK1, Bax, and caspase 3, and downregulation of AKT, NF-κB, Bcl-_XL expressions and some key oncomicroRNAs such as miRNA-21 and miRNA-200b significantly (p≤0.03). The results indicated the likelihood of the examined probiotic as an alternative or complementary treatment modality in signaling–targeted cancer therapy.