Antimicrobial peptides are distributed in all forms of life presenting activity against bacteria, fungi, viruses, parasites and cancer. In spite of the tremendous potential of these molecules, very few of them have been successfully developed into therapeutics. The major problems associated with this new class of antimicrobials are molecule stability, toxicity in host cells and production cost. A novel strategy to overcome these obstacles is conjugation to nanomaterials. Magnetic nanoparticles have been widely studied in biomedicine due to their physicochemical properties. The conjugation of antimicrobial peptides to magnetic nanoparticles could combine the best properties of both, generating an improved antimicrobial nanoparticle. Here we provide an overview and discuss the potential application of magnetic nanoparticles conjugated to antimicrobial peptides in overcoming diseases.