The design of novel multifunctional materials based on nanoparticles requires tuning of their magnetic properties, which are strongly dependent on the surface structure. The organic coating represents a unique tool to significantly modify the surface structure trough the bonds between the ligands of the organic molecule and the surface metal atoms. This work presents a critical overview of the effects of the organic coating on the magnetic properties of nanoparticles trough a selection of papers focused on different approaches to control the surface structure and the morphology of nanoparticles’ assemblies.