Ligand exchange on the surface of hydrophobic iron oxide nanoparticles is a common method for controlling surface chemistry for a desired application. Furthermore, ligand exchange with small-molecule ligands may be necessary to obtain particles with a specific size or functionality. Understanding to what extent ligand exchange occurs and what factors affect it is important for the optimization of this critical procedure. However, quantifying the amount of exchange may be difficult because of the limitations of commonly used characterization techniques. Therefore, we utilized a radiotracer technique to track the exchange of a radiolabeled C-14-oleic acid ligand with hydrophilic small-molecule ligands on the surface of iron oxide nanoparticles. Iron oxide nanoparticles functionalized with C-14-oleic acid were modified with small-molecule ligands with terminal functional groups including catechols, phosphonates, sulfonates, thiols, carboxylic acids, and silanes. These moieties were selected because they represent the most commonly used ligands for this procedure. The effectiveness of these molecules was compared using both procedures widely found in the literature and using a standardized procedure. After ligand exchange, the nanoparticles were analyzed using liquid scintillation counting (LSC) and inductively coupled plasma mass spectrometry. The labeled and unlabeled particles were further characterized by transmission electron microscopy (TEM) and dynamic light scattering (DLS) to determine the particle size, hydrodynamic diameter, and zeta potential. The unlabeled particles were characterized via attenuated total reflectance Fourier transform infrared spectroscopy (ATR FTIR) and vibrating sample magnetometry (VSM) to confirm the presence of the small molecules on the particles and verify the magnetic properties, respectively. Radioanalytical determination of C-14-oleic acid was used to calculate the total amount of oleic acid remaining on the surface of the particles after ligand exchange. The results revealed that the ligand-exchange reactions performed using widely cited procedures did not go to completion. Residual oleic acid remained on the particles after these reactions and the reactions using a standardized protocol. A comparison of the ligand-exchange procedures indicated that the binding moiety, multidenticity, reaction time, temperature, and presence of a catalyst impacted the extent of exchange. Quantification of the oleic acid remaining after ligand exchange revealed a binding hierarchy in which catechol-derived anchor groups displace the most oleic acid on the surface of the nanoparticles and the thiol group displaces the least amount of oleic acid. Thorough characterization of ligand exchange is required to develop nanoparticles suitable for their intended application.