We hypothesized that iron oxide NP with enzyme-like (peroxidase) activity catalyzes H2O2 to promote bacterial killing within dentinal tubules (DT) via in situ production of free radicals. We compared iron oxide NP bioactivity with currently used chemical modalities using confocal laser scanning microscopy (CLSM) and scanning electron microscopy (SEM) as analytical tools. The aim of this in vitro investigation was to use a recently developed Enterococcus faecalis infection model using root canal for evaluating iron oxide (Fe3O4) nanoparticles (NP) with biomimetic (catalytic) properties as a new antimicrobial endodontic treatment.