The formation of pathogenic biofilms on medical devices is a major public health concern accounting for over 65% of healthcare-associated infections and causing high infection morbidity, mortality, and a great burden to patients and the healthcare system due to its resistance to treatment. In this study, we developed a chitosan-based antimicrobial coating with embedded mesoporous silica nanoparticles (MSNs) to load and deliver eugenol, an essential oil component, to inhibit the biofilm formation of common bacteria in medical-device-related infections. The eugenol-loaded MSNs were dispersed in a chitosan solution, which was then cross-linked with glutaraldehyde and drop-casted to obtain coatings. The MSNs and coatings were characterized by dynamic light scattering, Brunauer-Emmett-Teller analysis, attenuated-total-reflectance Fourier transform infrared spectroscopy, X-ray photoelectron spectroscopy, 3D optical profilometry, and scanning electron microscopy. The release behavior of eugenol-loaded MSNs and coatings and the antibiofilm and antimicrobial activity of the coatings against adherent Staphylococcus aureus, methicillin-resistant S. aureus, and Pseudomonas aeruginosa were investigated. Eugenol was released from the MSNs and coatings in aqueous conditions in a controlled manner with an initial low release, followed by a peak release, a decrease, and a plateau. While the chitosan coatings alone or with unloaded MSNs demonstrated limited antimicrobial effects and still supported biofilm formation after 24 h, the coating containing eugenol not only reduced biofilm formation but also killed the majority of the attached bacteria. It also showed biocompatibility in indirect contact with NIH/3T3 fibroblasts and a high percentage of live cells in direct contact. However, further investigations into cell proliferation in direct contact are recommended. The findings indicated that the chitosan-based coating with eugenol-loaded MSNs could be developed into an effective strategy to inhibit biofilm formation on medical devices.