This review highlights the current situation of antimicrobial resistance and the use of magnetic nanoparticles (MNPs) in developing novel routes for fighting infectious diseases. The most important two directions developed recently are: (i) improved delivery of antimicrobial compounds based on a drastic decrease of the minimal inhibition concentration (MIC) of the drug used independently; and (ii) inhibition of microbial attachment and biofilm development on coated medical surfaces. These new directions represent promising alternatives in the development of new strategies to eradicate and prevent microbial infections that involve resistant and biofilm-embedded bacteria. Recent promising applications of MNPs, as the development of delivery nanocarriers and improved nanovehicles for the therapy of different diseases are discussed, together with the mechanisms of microbial inhibition.