Iron oxide nanoparticles (IONs) are one of the most developed and used nanomaterials in biotechnology and microbiology. These particles have unique physicochemical properties, which make them unique among nanomaterials. Therefore, many experiments have been conducted to develop facile synthesis methods for these particles and to make them biocompatible. Various effects of IONs on microorganisms have been reported. Depending on the microbial strain and nanoparticle (NP) concentration, IONs can stimulate or inhibit microbial growth. Due to the superparamagnetic properties of IONs, these NPs have used as nano sources of heat for hyper-thermia in infected tissues. Antibiotic-loaded IONs are used for targeted delivery of chemical therapy direct to the infected organ and IONs have been used as a dirigible carrier for more potent antimicrobial nanomaterials such as silver nanoparticles. Magnetic NPs have been used for specific separation of pathogen and non-pathogen bacterial strains. Very recently, IONs were used as a novel tool for magnetic immobilization of microbial cells and process intensification in a biotechnological process. This review provides an overview of application of IONs in different microbial processes. Recommendations are also given for areas of future research. ARTICLE HISTORY