The present study examined the anticancer capabilities of Bacillus coagulans supernatant-produced copper oxide nanoparticles (BC-CuONPs) on MCF-7 and SKBR3 cancer cells. The X-ray diffraction, ultraviolet–visible spectroscopy, Fourier-transform infrared spectroscopy, X-ray photoelectron spectroscopy, transmission electron microscopy, field-emission scanning electron microscopy, energy-dispersive X-ray, dynamic light scattering, and zeta potential techniques were used to characterize BC-CuONPs. This study also investigated the cellular and molecular processes of NPs’ anti-proliferative and apoptotic properties on human breast cancer cells and compared them to the commercial pharmaceutical tamoxifen. The size of the spherical NP was from 5 to 47 nm with negative zeta potential. The MTT results showed the great cytotoxic effect of BC-CuONPs against breast cancer cells. The BC-CuONPs inhibited the growth of breast cancer cells in a time- and dose-dependent manner. The up-regulation of BCL2-associated X (BAX), cyclin dependent kinase inhibitor 1A (P21), Caspase 3 (CASP3), and Caspase 9 (CASP9), the down-regulation of BCL2 apoptosis regulator (BCL2), Annexin V-FITC/propidium iodide, and reactive oxygen species (ROS) generation results suggested that BC-CuONPs had a significant apoptotic impact when compared to the control. Scratch tests and vascular endothelial growth factor receptor gene (VEGF) down-regulation demonstrated that BC-CuONPs had anti-metastatic activity. The cell cycle analysis and down-regulation of Cyclin D1 (CCND1) and cyclin dependent kinase 4 (CDK4) revealed that cancer cells were arrested in the sub-G1 phase. Finally, the results showed that the secondary metabolites in the supernatant of Bacillus coagulans could form CuONPs, and biogenic BC-CuONPs showed anti-metastasis and anticancer properties on breast cancer cells while having less adverse effects on normal cells. Therefore, the synthesized CuONPs using B. coagulans supernatant can be shown as a potential candidate for a new therapeutic strategy in cancer management.