As a leading global cause of mortality, cancer continues to pose a significant challenge. The shortcomings of prevalent cancer treatments, such as surgery, radiation therapy, and chemotherapy, necessitate the exploration of alternative therapeutic strategies. Selenium nanoparticles (SeNPs) have emerged as a promising solution, with their synthesis being widely researched due to their potential applications. Among the diverse synthesis methods for SeNPs, the green chemistry approach holds a distinctive position within nanotechnology. This research delves into the anti-proliferative and anticancer properties of green-synthesized SeNPs via the cell-free supernatant (CFS) of Lactobacillus casei (LC-SeNPs), with a specific focus on MCF-7 and HT-29 cancer cell lines. SeNPs were synthesized employing the supernatant of L. casei. The characterization of these green-synthesized SeNPs was performed using TEM, FE-SEM, XRD, FT-IR, UV-vis, energy-dispersive X-ray spectroscopy, and DLS. The biological impact of LC-SNPs on MCF-7 and HT-29 cancer cells was examined via MTT, flow cytometry, scratch tests, and qRT-PCR. Both FE-SEM and TEM images substantiated the spherical shape of the synthesized nanoparticles. The biosynthesized LC-SNPs reduced the survival of MCF-7 (by 20%) and HT-29 (by 30%) cells at a concentration of 100 μg/mL. Flow cytometry revealed that LC-SNPs were capable of inducing 28% and 23% apoptosis in MCF-7 and HT-29 cells, respectively. In addition, it was found that LC-SNPs treated MCF-7 and HT-29 cells were arrested in the sub-G1 phase. Gene expression analysis indicated that the expression levels of the CASP3, CASP9, and BAX genes were elevated after treating MCF-7 and HT-29 cells with LC-SNPs. Further, SeNPs were observed to inhibit migration and invasion of MCF-7 and HT-29 cancer cells. The SeNPs, produced via L. casei, demonstrated strong anticancer effects on MCF-7 and HT-29 cells, suggesting their potential as biological agents in cancer treatment following additional in vivo experiments.