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The present study evaluated the properties and ochratoxin A (OTA) degradation capacity of the dietary probiotic <i>Pediococcus pentosaceus</i> BalaMMB-P3, isolated from a milk coagulant. The acidic tolerance of the isolate at pH 2–3 was checked with bile salts. No hemolytic activity was noted, which confirmed the nonpathogenicity of the strain. The isolate was tested in vitro for antibiotic susceptibility, enzymatic activity, bile salts hydrolase activity and antifungal activity against <i>Penicillium verrucosum</i>, <i>Fusarium graminearum</i> and <i>Aspergillus ochraceus</i>. A molecular docking-based OTA toxicity assessment was carried out for multitargeted proteins. The 16S rRNA gene-based phylogenetic assessment identified the strain as <i>P. pentosaceus,</i> and was authenticated in GenBank. The carboxylesterase and glutathione s-transferase enzymes showed active and strong interactions with esters and amide bonds, respectively. The compound exhibited carcinogenic and cytotoxicity effects at an LD₅₀ value of 20 mg/kg. Furthermore, the strain showed a potent ability to reduce OTA and suggested the prospects for utilization in nutritional aspects of food.