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The rising threat of multidrug-resistant Bacillus cereus has compromised treatment efficacy, necessitating alternative solutions. Cecropins, peptide antibiotics, may offer promise, but research on their efficacy against MDR B. cereus is limited, highlighting a critical knowledge gap in addressing this public health concern and food safety issue. This study investigated the prevalence of B. cereus in powdered soybean and evaluated the antibacterial activity of cecropins, antimicrobial peptides derived from the gut of Macrotermes termites, against isolated strains. A total of 100 powdered soybean samples were collected from retail outlets in Awka Metropolis and screened using standard microbiological techniques. Cecropins were obtained via solvent extraction and chromatographic purification, and their inhibitory activity was assessed using an agar-well diffusion method. Molecular analysis identified three B. cereus strains: FORC6 (BCFOR), DQ01 (BCDQO), and CD3 (BCCD3), with BCFOR being the most prevalent (p < 0.05). Antibiotic susceptibility testing revealed multidrug resistance, particularly in BCCD3 (75%), highlighting the limitations of conventional antibiotics. Cecropins exhibited concentration-dependent inhibitory activity against all isolates, with BCCD3 showing the highest susceptibility, followed by BCDQO and BCFOR. The results suggest that cecropins have potential as a natural biocontrol agent in food systems. These findings have important implications for food safety and the development of novel antimicrobial strategies targeting multidrug-resistant foodborne pathogens.