Microorganisms in biofilms are protected from environmental stressors and therefore exhibit strong resistance to conventional removal strategies, including chemical disinfectants and antibiotics. In this study, we systematically evaluated nanomaterial-based removal methods on Listeria innocua biofilms. Anisotropic magnetic particles, composed of iron oxide, and silver nanoparticles, known for their intrinsic antibacterial properties, were used to assess the potential of nanostructure-triggered biofilm disruption. We investigated how particle surface roughness and size affect biofilm removal under magnetic actuation, using both classical colony-forming unit quantification (viability assessment) and fluorescence-based detection via a reporter protein. The surface roughness and size of anisotropic magnetic particles only modestly affected biofilm disruption. Conversely, a synergistic effect was observed when anisotropic magnetic particles were grafted with silver nanoparticles. Furthermore, we used Enterococcus faecalis and Candida albicans biofilms and observed pronounced species-dependent variability of the silver-based treatments. Our results indicate that hybrid magneto-chemical strategies represent a promising and likely necessary approach for reliable and robust biofilm removal.