The impact of bacterial microbiome metabolites on human health, most particularly on the prevention and treatment of cancer, has gained significant interest in recent times. The study focused on the isolation of bacterial flora associated with the ovaries of 8-week-old mice and examined its ability to produce metabolites with potential antibacterial, antioxidant, and anticancer properties. The isolates were identified based on biochemical and 16S rRNA sequencing. The ethyl acetate extract from isolates was screened for antimicrobial and antioxidant capacity. The 3-[4,5-dimethylthiazole-2-yl]-2,5-diphenyltetrazolium bromide (MTT) assay was used to evaluate the cytotoxicity of the selected isolate against the ovarian carcinoma cell lines SKOV-3 and PA-1. The ethyl acetate extract from Bacillus velezensis OM03 exhibited significant antibacterial activity against all the tested bacteria, with a MIC value ranging from 50 to 100 µg/mL. Furthermore, the extracts demonstrated hydrogen peroxide and 2, 2-diphenyl-1-picrylhydrazyl (DPPH) scavenging activities at rates of 88.50% and 87.78%, respectively. The extracts displayed substantial concentration-dependent antiproliferative/cytotoxic activities against SKOV-3 and PA-1 cell lines after 24 and 48 h of treatments, respectively. Further chemical analysis of the extract using HR-LCMS revealed the presence of bioactive compounds such as myriocin, 2,3-diethylpyrazine, dihydrodeoxystreptomycin, cyclo (L-Phe-L-Pro), C16 sphinganine, and other twenty-nine compounds that have been formerly reported and are accountable for the targeted activities. Bacillus velezensis OM03 may be further investigated for the creation of novel therapeutics, particularly for the treatment of ovarian cancer.