Biofilms that form on reusable medical devices are a cause of hospital acquired infections; however, sanitization of biofilms is a challenge due to their dense extracellular matrix. This work presents an innovative strategy using biocide-loaded iron oxide nanoparticles transported within the matrix via a magnetic field to eradicate biofilms. Results show that the active delivery of the biocide to underlying cells effectively penetrates the extracellular matrix and inactivates Methicillin resistant Staphylococcus aureus (MRSA) biofilms (responsible for several difficult-to-treat infections in humans). To optimize this treatment, the loading of spherical, cubic and tetrapod-shaped nanoparticles with a model biocide, CTAB (cetyltrimethylammonium bromide) was studied. Biocide loading was determined to be dependent on the shapes' surface charge density instead of the surface area, meaning that biocide attachment is greater for nanoparticles with sharp edges (e.g. cubes and tetrapods). These results can be used to optimize treatment efficacy, and help further understanding of biofilm and nanoparticle surface zeta potentials, and the nanoparticle-biofilm interactions.