In this work, the soft-template technique was employed in preparing the superparamagnetic Fe3O4 nanoparticles from natural iron sand. A series of the Fe3O4 nanoparticles formed spinel crystal structure with the particle size in the range of 1.9 to 6.6 nm which was varied by diethylamine concentration as the template. All samples had the functional groups of Fe3+-O2−, Fe2+-O2− and OH and exhibited the superparamagnetic character. The antibacterial activity of the Fe3O4 nanoparticles showed a significant outcome to pathogen growth rate. Pre-administration of bacterial stock solution (E. coli and B. substilis) with magnetite significantly reduced the colony formation compared to control group. In particular, for Gram-negative bacteria growth rate, pretreatment with magnetite declined the colony formation considerably compared to placebo and positive control group. Also, in line with Gram-negative bacteria, the similar pattern of the bacterial killing property was observed in Gram-positive bacteria.