The increasing morbidity and mortality of infectious diseases is an increasing concern. Despite the continuous development and synthesis of new antimicrobial drugs, microbial pathogens are exhibiting increased multi-drug resistance. Nanomaterials display unique and well-defined physical and chemical properties including a very high surface area to volume ratio, and new approaches for antimicrobial therapies have attempted to combine nanomaterials and current antimicrobial drugs. Magnetic nanoparticles (MNPs) are characterized by biocompatibility, biodegradation, and safety for human ingestion. Iron oxide nanoparticles have been approved for human use by the US Food and Drug Administration (FDA). For biomedicine applications, MNPs require surface modification to become water-soluble and be stable enough to resist the effects of proteins and salts in the physiological environment. MNPs can combine various substrata, such as biomolecules and nanomaterials to generate new antimicrobial agents which combine antibacterial, antiviral, and antifungal properties. This can be accomplished through a series of surface modification methods. Because MNPs have unique superparamagnetic characteristics, they can be controlled and recycled by an external magnetic field.In addition, the antimicrobial activity of MNPs-based nanocomposites is superior to that of metallic nanoparticles. This paper reviews the recent literature on the use of MNP-based nanomaterials in antimicrobial applications in biomedicine. Antimicrobial applications mainly focus on inhibiting and killing bacteria and fungi and viruses inactivation. The synthesis, surface modification, and characteristics related to MNPs will also be briefly addressed.