Safe implementation of nanotechnology-based products in biomedical applications necessitates an extensive understanding of the (bio)transformations that nanoparticles undergo in living organisms. The long-term fate in the body is a crucial consideration because it governs potential risks for human health. To accurately predict the life cycle of nanoparticles, their fate after administration into the body-including their (bio)transformations, persistence, and biodegradation-needs to be thoroughly evaluated. Magnetic iron oxide nanoparticles (MIONPs) can enter the body through various routes, including inhalation, ingestion, dermal absorption, and injection. Microscale and nanoscale studies are performed to observe nanomaterial biotransformations and their effect on clinically relevant properties. Researchers are utilizing high-resolution TEM for nanoscale monitoring of the nanoparticles while microscale follow-up approaches comprise quantification tools at the whole organism level and the molecular level. Nanoparticle-cell interactions, including cellular uptake and intracellular trafficking, are key to understanding nanoparticle accumulation in cells and organs. Prolonged accumulation may induce cell stress and nanoparticle toxicity, often mediated through oxidative stress and inflammation. In this review article, the journey of nanoparticles in the body is depicted and their biotransformations and final fate are discussed. Immunohistochemical techniques are particularly valuable in tracking nanoparticle distribution within tissues and assessing their impact at the cellular level. A thorough description of a wide range of characterization techniques is provided to unveil the fate and biotransformations of clinically relevant nanoparticles and to assist in their design for successful biomedical applications.