This paper verified the possibility of applying chitosan and/or ferulic acid or polycaprolactone (PCL)-based coatings to polydimethylsiloxane/neodymium–iron–boron (PDMS/NdFeB) composites using the spin-coating method. The surface modification of magnetic composites by biofunctional layers allows for the preparation of materials for biomedical applications. Biofunctional layered magnetic composites were obtained in three steps. The spin-coating method with various parameters (time and spin speed) was used to apply different substances to the surface of the composites. Scanning electron microscopy (SEM) and confocal laser scanning microscopy (CLSM) were used to analyze the thickness and surface topography. The contact angle of the obtained surfaces was tested. Increasing spin speed and increasing process time for the same speed resulted in decreasing the composite’s thickness. The linear and surface roughness for the prepared coatings were approximately 0.2 μm and 0.01 μm, respectively, which are desirable values in the context of biocompatibility. The contact angle test results showed that both the addition of chitosan and PCL to PDMS have reduced the contact angle θ from 105° for non-coated composite to θ~59–88° depending on the coating. The performed modifications gave promising results mainly due to making the surface hydrophilic, which is a desirable feature of projected biomaterials.