Potato peel waste (PPW) represents a low-cost and eco-friendly by-product with potential for use as a fermentation substrate for the production of antibacterial metabolites by Bacillus species. This study evaluated PPW as a fermentation matrix for Bacillus velezensis and demonstrated that 2% PPW supported optimal production of antibacterial compounds. The cell-free supernatant obtained after 96 h of fermentation exhibited the strongest activity against E. coli 18/22, with a MIC of 62.5 µg/mL. The ethyl acetate extract exhibited rapid bactericidal activity, killing E. coli 18/22 within 30 min at 2× MIC and within 120 min at MIC. The antibacterial activity remained stable up to 80 °C, across pH 4–12, and after treatment with pepsin and chymotrypsin. LC/HR-ESI-MS analysis identified oxydifficidin and surfactins C14 and C15 as the main active compounds. Molecular docking revealed that oxydifficidin and surfactin C15 exhibited the strongest binding affinity toward Shiga toxin II, while surfactin C14 displayed a weaker interaction, suggesting the role of acyl chain length in toxin binding. Both oxydifficidin and surfactins interacted with key residues within the catalytic pocket of the AcrB subunit of the AcrAB–TolC multidrug efflux pump, indicating potential inhibition of multidrug resistance mechanisms. To our knowledge, this is the first report describing the use of PPW as a fermentation substrate for Bacillus velezensis B38 to produce oxydifficidin and surfactin C14 and C15 exhibiting antimicrobial activity against multidrug-resistant E. coli. These findings provide a promising strategy for transforming agro-industrial waste into value-added antimicrobial metabolites, contributing to the circular bioeconomy strategies within the One Health framework.