Antibiotic resistance (AMR) is one of the pressing global public health concerns and projections indicate a potential 10 million fatalities by the year 2050. The decreasing effectiveness of commercially available antibiotics due to the drug resistance phenomenon has spurred research efforts to develop potent and safe antimicrobial agents. Iron oxide nanoparticles (IONPs), especially when doped with metals, have emerged as a promising avenue for combating microbial infections. Like IONPs, the antimicrobial activities of doped-IONPs are also linked to their surface charge, size, and shape. Doping metals on nanoparticles can alter the size and magnetic properties by reducing the energy band gap and combining electronic charges with spins. Furthermore, smaller metal-doped nanoparticles tend to exhibit enhanced antimicrobial activity due to their higher surface-to-volume ratio, facilitating greater interaction with bacterial cells. Moreover, metal doping can also lead to increased charge density in magnetic nanoparticles and thereby elevate reactive oxygen species (ROS) generation. These ROS play a vital role to disrupt bacterial cell membrane, proteins, or nucleic acids. In this review, we compared the antimicrobial activities of different doped-IONPs, elucidated their mechanism(s), and put forth opinions for improved biocompatibility.