The preparation of biocompatible magnetic polymer nanoparticles of controlled size and uniform size distribution is of great interest for bio-applications, such as drug delivery. Such particles can combine the benefits of nanoparticles made of biodegradable and biocompatible polymers with the superparamagnetic properties conferred by magnetic nanocrystals encapsulated into them. However, the preparation of such particles is a challenging task. In this work, we present an innovative and clean process that allows one to prepare submicron monodispersed poly(lactic-co-glycolic) acid (PLGA) particles containing high loads of magnetite nanocrystals. First, hydrophobic magnetite nanocrystals are prepared through a coprecipitation reaction from iron chlorides solutions in alkaline conditions, with oleic acid used as capping agent. Then, magnetite nanocrystals and PLGA are first dispersed together in dichloromethane, and subsequently emulsified water in the presence of polyvinyl alcohol (PVA) as stabilizer. The organic solvent is finally removed by extraction with supercritical carbon dioxide sCO2. This last step is accomplished by spraying the emulsion through a nozzle into a high pressure vessel containing the sCO2. This step can be carried out both in batch or continuous operation modus. The result is a stable suspension of PLGA particles in water with a narrow size distribution. The initial composition of the organic phase determines both the magnetite loading as well as the size of the nanoparticles, which is however strongly dependent on the emulsification process and the corresponding droplet size before the extraction. The nanoparticles have been characterized by light scattering and transmission electron microscopy.