In this manuscript we demonstrate the spatially controlled immobilization of ferritin proteins by directly writing them on a wide range of substrates of technological interest. Optical and fluorescence microscopy, AFM and TOF-SIMS studies confirm the successful deposition of the protein on those surfaces. Control on nanostructure shape and size, by miniaturizing the dot-like features down to a 100 nm, demonstrates the particular capabilities of the DPN approach. Ultimately, this study gives the opportunity to design nanoparticle-based arrays regarding the growing interest in the use of nanoparticles as structural and functional elements for fabricating nanodevices. Herein, we demonstrate how the protein shell of ferritins can be removed by a simple heat-treatment process while maintaining the encapsulated inorganic nanoparticle intact on the same location of the nanoarray. As a result, this study establishes how direct-write DPN approach could give the opportunity to design not only protein-based nanoarrays but also nanoparticle-based nanoarrays with high-resolution and control.