Microbial contamination and biofilm formation on food contact materials (FCMs) represent critical challenges within the food supply chain, compromising food safety and quality while increasing the risk of foodborne illnesses. Traditional materials often lack sufficient microbial resistance to contamination, creating a high demand for innovative antimicrobial surfaces. This study assessed the effectiveness of a nanosized deposited SiOxCyHz coating approved for food contact on 3D-printed polyamide 12 (PA12) disk substrates, aiming at providing antimicrobial and anti-biofilm functionality to mechanical components and packaging material in the food supply chain. The coating was applied using plasma-enhanced chemical vapor deposition (PECVD) and characterized through Fourier-transform infrared spectroscopy (FTIR), Raman spectroscopy, thermogravimetric analysis (TGA), scanning electron microscopy (SEM), and contact angle measurements. Coated PA12 samples exhibited significantly enhanced hydrophobicity, with an average water contact angle of 112.9°, thus improving antibacterial performance by markedly reducing bacterial adhesion. Microbiological assays revealed a significant (p < 0.001) bactericidal activity (up to 4 logarithms after 4 h, ≥99.99%) against Gram-positive and Gram-negative bacteria, including notable foodborne pathogens such as L. monocytogenes, S. aureus, E. coli, and S. typhimurium. SiOxCyHz-coated PA12 surfaces exhibited strong antibacterial activity, representing a promising approach for coating additive-manufactured components and equipment for packaging production in the food and pharmaceutical supply chain able to enhance safety, extend product shelf life, and reduce reliance on chemical sanitizers.