The data presented in this article are related to the publication entitled "Iron oxide core oil-in-water nanoemulsion as tracer for atherosclerosis MPI and MRI imaging" (Prévot et al., 2017) [1]. Herein we describe the synthesis and the characteristics of the Superparamagnetic Iron Oxide Nanoparticles (SPION) loaded inside nanoemulsions (NEs). Focus was set on obtaining SPION with narrow size distribution and close to superparamagnetic limit (20 nm) in order to reach a reasonable magnetic signal. Nanoparticles (NPs) of three different sizes were obtained (7, 11 and 18 nm) and characterized using transmission electron microscopy (TEM), X-ray diffraction (XRD), vibrating sample magnetometer (VSM), diffuse reflectance infrared Fourier transform (DRIFT) and thermogravimetric analysis (TGA). SPION were coated with oleic acid (OA) in order to load them inside the oily core of NEs droplets. SPION loaded NEs were magnetically sorted using MACS® MS Column (Miltenyi Biotec) and iron quantification was performed by UV-spectrometry measurements.