Mycotoxins are the potent toxic chemical agent's linked to food safety, pose a serious risk to human and animal health globally. The management of toxigenic fungi is a challenging task in food and feed industries. The present investigation aimed to use probiotic potentials of lactic acid bacteria (LAB), and fermented cell-free broth as antifungal agents and neutralization of carcinogenic mycotoxin, fumonisin B1 (FB1) in food and feed considered as “turned waste into treasure”. We strived to investigate the probiotic potential of Lactococcus lactis subsp. lactis BIONCL17752 strain on prevention of growth and neutralization of FB1 produced by Fusarium verticillioides BIONCL4 strain to emulate as as a food grade bio-preservative. The BIONCL17752 strain exhibited excellent inhibitory activity against BIONCL4 strain. It was cultivated in MRS medium, and obtained cells pellet (CP) and cell-free supernatant (CFS) was lyophilized, and used for their antifungal activity against BIONCL4 strain. The minimum fungicidal concentration (MFC) determined as 12.5 μg/mL. Nevertheless, CFS assessed for neutralization of FB1 production which exhibited complete inhibition and downregulation of FB1 encoding FUM1 gene expression using quantitative real-time PCR (qPCR). Furthermore, CFS induced transcriptomic studies against BIONCL4 strain endorsed a significant downregulation of virulence, FB1, fusaric acid, fusarin, and chitin biosynthetic pathway genes. The CFS and cells reticent spore germination and FB1 production in the range of 40–61% and 74–85%, respectively under stored maize for 60 days. The current findings suggest BIONCL17752 strain apprehend the fungal growth and inhibit the FB1, and other toxigenic molecules biosynthesis, and can be employed as food grade preservative in the food industries to ensure the food safety and human health.