Magnetic nanoparticles (MNPs) represent one of the most promising materials as they found application in bionanotechnology for enhanced imaging, diagnosis, and treatment of various diseases. Silica improves colloidal stability and the binding affinity for various organic molecules and as such is used to cover iron oxide NPs. One of the strategy for improving the coated MNPs might be the functionalization with organic molecules, such as cell penetrating peptides (CPPs) since they are able to enter into the cells and can enhance the physicochemical properties, adding a cell penetrating feature of the MNPs. In this work, a computational investigation on several CPPs interacting with three different silica surfaces is presented.